First Insanity trilogy playthrough advice

My favorite ME3 SR is the Indra for all classes, followed by the Valiant. The Indra is in a DLC weapons pack and the Valiant is a collectors edition gun.

I usually carry 2 weapons, my SR and an SMG - but the Indra has a really large ammo capacity (180+ shots), so I've never actually needed to take the SMG out due to running out of ammo. The Indra doesn't deal a lot of damage per shot, so it can sometimes take a whole clip (25 shots) to take down an enemy with protection on insanity. The Valiant has only a +30-shot ammo capacity, but, even so, I have only very rarely run out of ammo on it. I think the Viper's ammo capacity is about 48 shots, so you're probably OK and won't run out if you're decently accurate. Still, a light SMG or light pistol with an Ultralight materials mod on it effectively weighs almost nothing... so, I figure, why not have one along just in case?

As for triggering a tech burst, I don't think that the shields have to come right off before you can hit them with incinerate to trigger the burst and cause damage to the shields of nearby enemies. With my current infiltrator, I know I've just hit a turret with EDI's overload and it still had some shields left and incinerate was showing up in red, but I hit the turret with it anyway and the turret exploded taking out the engineer standing beside it (level 59 infiltrator on insanity - Chronos mission). I did also have squad cryo modded ammo on, so not sure if that would make a difference. Unfortunately, if I hit any lesser shielded mook with EDI's overload at this level, the shields are gone in that first hit, so I can't really say whether or not they need to be gone or whether some shield needs to still be there... my squad is just being to danged efficient right now ripping through these guys before I even really get a chance for a fair test for you.

The Indra is great is the SR really is your primary weapon. I used to run with it a lot. It's great because it's useful against every type of enemy, even the mooks because the rather light damage and huge ammo capacity makes it possible to dish out damage in just the right dosage without pointless overkill.
However, at some point, I moved on to using SRs really as specialty weapons against tough opponents or when the terrains promotes sniping. For that, I think the black widow is the ideal compromise between high damage and decent ammo capacity. You can shoot a mook in a pinch without feeling bad about wasting the bullet but it's damage is high enough so that it also makes short work of tough enemies like Banshees.
However, do expect to use a secondary weapon in close quarters or against swarms of low level opponents. I usually take an AR for that. Love the constant stream of fire (especially if I have sniper rifle with few but hard punches) and with an AR, Shep just looks so much more like he means business than with those measly SMGs, hehe. Maybe a pistol or SMG would technically be the smarter choice but Shepard's armor just looks like 2 rifles belong on it's back.

The combination is also good against high level tech opponents since ARs are very effective against shields and SRs are great against armor.

You are right, for excessive power users, the weight is definitely an issue with my usual combination. It works for me because I mainly use tactical cloak for positioning or maybe an incinerate or shield drain once in a while but I tend to shoot a lot, so I don't mind the recharge penalties that much. In fact, I find the the recharge times insane if you just use lighter weapons. Compare to what I was used to from ME1/2, I can barely keep up spamming all those powers with that super fast recharge.

Thanks guys for the input - will look out for the Indra (don't have it yet) - one more follow-up. How much does upgrading a weapon from like Indra 1 to Indra 5 matter? Costs me like ~15k credits to go from 1-5 for any weapon. I feel like I've been blowing some dough on weapons I won't use (like maybe the Viper.)

I'll consider an SMG then as a second weapon - or AR if I can get the wep light enough via mods. What's the diff mainly b/t SMG and AR damage-wise? Also which SMGs/ARs would you recommend? Also I'm not using Sabotage much - mainly Overload/Incin or Incin/Incin - am I missing out on some good combos?

I've got EDI now and we're doing Grissom (last part) - what's odd is, Garrus and EDI are trapped behind the door that leads into the atrium LOL - I can still use their powers but I'm not getting any weapon damage. I remember this happened last time I played - a bug?

No, the weapon has to be in your hands for those mods to take effect.

The cost varies a bit depending on the weapon.  When you look at the terminal, the ones near the top of the list will level up more cheaply than the ones near the bottom.  I find I easily have enough to fully upgrade about 6 weapons to Level V (or X in an NG+ playthrough).  If you have the Citadel DLC, there are ways you can get your hands on a lot of extra credits by playing in the combat sim over and over again (10,000 credits for a Gold prize) or you can gamble in the casino (a lucky all-in bet at the roulette table can net you over 25,000 credits... but to turn that into a money mill, you'll have to be prepared to save and reload in order to cut your loses; that is, the combat sim is the most reliable money source).  I've heard of some people spending hours there and eventually earning enough credits to level up every weapon in the game.

If you don't have the Indra, it means that you haven't purchased the DLC Firefight weapons pack.  I don't think the pack is very expensive at all and this weapon is well worth it.  It's not a weapon you can collect in the game, but it should be available immediately if you buy the DLC.  The best in-game (stock) SR, IMO, is the Black Widow (purchase from Spectre Requisitions), but it's a heavy brute.  It does phenomenal damage and can fire 3 rounds before reloading.  The M98 Widow does almost as much damage, is a tad lighter, but does need to be reloaded after every shot (some people do use a bit of a glitch to short-circuit the loading animation and reduce the reload time).  Beyond that, you should be picking up the Raptor when you get to Sur'Kesh, which is a bit of a boost over the Viper but along the same lines... so you might like it.

I've never experienced anyone getting stuck during Grissom, but that sure sounds like a bug to me.

I guess I'm the only one who doesn't use a sniper rilfe in my playthroughs. Except for the one playthrough where I used one for the whole playthrough. I ended up firing from the hip more than scoping down an enemy.

Just buy it already... you know you want it!.   (You can always do a few rounds in the combat sim to get more credits.  I also like using the combat sim to test out different weapons and mods much better than the shooting range, IMO.)

What level is your sabotage at?  I find hacking the turrets in a level like the Atrium to be very helpful as CC.  You can also sabotage the mech.  Even if you don't combo it afterward, it will stop firing at you for a brief time.

I am a little late to reply, but here goes:

1. I use the Viper on my sniper Engineer. It is a lightweight weapon with decent-ish damage, quick reload, and with Ashley's squad disruptor ammo it can prime for a tech burst on every shot.

1b. You do not need two weapons. No class needs two weapons. As long as you continue to use power combos, you will never run out of ammo. And the engineer does not really care about ammo/weapons since you get through the whole game without needing to fire your weapon except in very specific situations.

2. You do not need to fully strip shields with Overload to prime for a tech burst. Overload will prime for a tech burst after hitting health/armor/shields/barrier, and will last for 3 or 5 seconds. (It was 3 seconds at launch, then multiplayer got patched later to increase the priming window to 5 seconds; I don't know if single player benefitted from that buff).

Overload > Incinerate = Tech burst. Overload priming window lasts 3 or 5 seconds as mentioned above.
Incinerate > Overload = fire explosion. it takes about 0.5 seconds after hitting Incinerate before the enemy is primed for a fire explosion. Priming window lasts about 3 seconds.
Sabotage (backfire) > Overload/Incinerate = Tech burst. Sabotage activates 1.5 seconds after Sabotage hits the enemy. Priming window lasts 2 seconds.

I prefer using Sabotage > Overload as my main power combo on most enemies.

You can chain Overload > Incinerate > Overload > Incinerate on the toughest enemies (Atlas mechs, Geth Primes, Banshess, and so on) for alternating tech bursts and fire explosions, which is why I like using Sabotage > Incinerate > Overload on these enemies. 

The atrium fight can be tough, but it still should have been quite manageable at the level you're at.  As themikefest suggested, heading directly for the high ground helps as well.  If you get stuck down below, it's easier to either get overwhelmed or get hit by one of the rockets coming from the atlas.  Your difficulty may well be that you are just very used to having Liara there for her singularity (which is very effective for getting the guardians to drop their shields).  You can certainly take her with you as an Engineer and combine her with Garrus or EDI... that way you'll still have one squad mate to play off for overload/incinerate combos.  If it suits your own playstyle better... go for it.

I do throw EDIs "excess" points into her decoy skill, but I've never really seen where it has done too much.  With the explosive iteration, there is a slight chance the decoy will do some damage, but it's not really reliable since it doesn't go after enemies the same way the drones to and enemies don't tend to get in too close to it either.  I have seen it occasionally draw some fire away from Shepard, but overall it's kind of underwhelming.

I was thinking the drone at Rank 6 w/ the evolution to zap a few enemies might be useful. I guess not. Could re-spec points into a level 6 Flamethrower. Dang, I liked the idea of the drones/turrets but it seems in their execution it isn't that good.

I'm realizing now I'm relegated to Overload/Incin/Sabotage - is that fun enough as an Engineer? Kind of a little let down the bots aren't really useful (as people have said.) It's not too late for me to start over I guess as something else but maybe I should give it a little more time? Any suggestions?

Is there a way I could get 2 squadmates that help with with Incin/Overload AND help detonate Biotic explosions. Hmmm...