weaponless vessels in MEA2...?

. Except with mass effect field it doesn't have a mass worth talking about, that's kinda the point, it regains mass after it leaves the field

The only thing Arming those 5 ships would have done is get them slaughtered. The Archon had a full Invasion fleet, and we weren't invading Heleus. At the time they launched the Initiative had every reason to believe the cluster was devoid of advanced technology. Not to mention their resources were not infinite, they barely had the means to transport their colinists let alone out fit the arks with full blown siege technology, and again they weren't on their way to fight a war. They had no reason to assume they would be assaulted in such a way.

Their issues in the cluster weren't due to a lack of weaponry, they were due to the scourge (which weapons wouldn't have assisted against) and completely unknown technology being hit by the scourge and rendering all of their planets inhabitable.

Had those ships been armed to the teeth they still wouldn't have been able to defend themselves against the Archon's Armada, there's no situation where they're NOT boned coming out of 634yr cryo sleep against a full scale invasion fleet capable of subjugating an entire cluster. (An invasion fleet that had only been there a fraction of the time of their journey.) Armed ships or not, the only thing that would have saved them in that instance would be finding allies. It would have been pure stupidity to fire upon such a fleet, suicide. Especially since Humans are unfit for exaltation, there would have been no reason to swat that bee out of the air.

As far as the potential of small skirmishes, pirates and raiders? They were actually WELL equipped to handle them... And they did. The colonists were not defenseless, they were just not prepared for a war they had no way of knowing would be going on.

The Nexus and the Arks also had plenty of people to stop boarding parties, but unfortunately the Nexus skeleton crew was fractured by infighting losing a large portion of their crew and nearly all of their Krogan. The Arks themselves were unable to fight back not due to a lack of shipbased weaponry (again, not enough to destroy a full Invasion fleet) but due to the fact that nearly all of their people are stuck in cryo because their Golden world can't support them.

As far as the ideal itself? The mission isn't some "Kumbaya" expedition. Its one of compassion and scientific progression. They're reaching out in PEACE, to make allies and further their understanding of the Universe. They're explorers trying to AVOID the mistakes of the First Contact War, not recreate them.

1. Expecting trouble is not the same as expecting an Armada equipped to Exalt an entire cluster. Dangerous wildlife, pirates, those things were anticipated and accounted for, and handled with little trouble despite the majority of their people being in stasis. They surveyed THOUSANDS of planets in Andromeda and settled on the Heleus cluster. Had they seen evidence of an aggressive force on that scale they simply would have chosen to go elsewhere. They accounted for realistic problems efficiently: to quote "We expected Hostilities, not an enemy that wouldn't even speak." 

2. That's a matter of opinion (and an incredibly biased one.) Kett Weaponry and technology is stated several times to be on par with MW tech (stated IN GAME to be superior in some ways.) The only way a Kett ship would be "scrap" is just because you think they don't look as fancy. Even if they were significantly inferior to Initiative MW craft, five well armed ships STILL would not Trash an entire Armada. That is incredibly biased wank.

3. The ship's greater size was for the very specific reason of transporting in excess of 20k colonists, supplies, outpost materials, and survey equipment each 2million light years. No faction I've seen in any game in the series has had such limitless resources that they could retrofit an unprecedented ship like that into a warship as well, not to mention the time constraints on the project. Its more complicated than "Well why CAN'T it be a gigantic warship TOO!" A buss is larger than some tanks, but that doesn't mean slapping a couple of guns on it will make it a fair fight. Cargo planes are larger than fighter jets, you should be getting my point by now.

4. As I stated very clearly before, the reason these ships were successfully boarded had very little to nothing at all to do with the lack of armament. They were all running skeleton crews, unable to bring the bulk of their crew out of stasis. 20 thousand, even poorly if that had been the case, armed civilians would be enough to deter any boarding party. The main problems they encounter are a lack of habitable planets, the scourge, leading to a lack of resources and thusly manpower.

Yeah, I think the gameplay/encounter design was a big chunk of the reason. We weren't dealing with turrets, geth colossus, or the like, though there is some sizable wildlife.

Another reason I suspect has to do with controller mapping. The Mako and Hammerhead were controlled with the left stick, just like walking. They clearly wanted to make the Nomad a much sportier vehicle, and making it fun to drive was a high priority. Acceleration/deceleration is now mapped to the triggers (which were used to fire the Mako's and Hammerhead's weapons) instead of the left stick - which I suspect lends greater control of the vehicle. I've never played a racing game, but I think the Nomad's control mapping is more in line with vehicle controls from other games, so driving it feels more natural to those who have played those other games. Anyway, the triggers that are usually used to fire weapons have been assigned to moving the vehicle, so... perhaps that's another reason why the Nomad is weapon-free.

On another note:

I have to wonder what might have happened if the arks did have weapons that autofired on the scourge, with it being dark energy and all? There are quite a few possibilities I can imagine, and most of them result in the ark taking much more damage. I dunno.

You're using highly selective logic and leaving out serious details in order to support your stance. The game detailed these issues clearly, as have I.

The issue isn't with plot screening writer logic, its with you being unable to understand the many thought processes that would go into an endeavour like this because you just want to blow shit up. That's okay, this isn't the game for you. That doesn't mean the game is wrong in the slightest though.

I'm not so sure that the controller layout was an issue. The cannon used the R1 bumper in ME. That's used for mining probes in MEA, but only when that mode is activated. They could've implemented a functional weapon, but I don't necessarily think they should have. Your point about the Nomad being a light, agile vehicle is important. It couldn't support a big gun, or even one that could seriously trump combo explosions. Plus, as we mentioned with gameplay, that would be cheap and boring as hell. I like to earn my victories; not roll up and blast 10 dudes with a cannon or mini-gun.

The exploration vehicle fit the game very well, I think. I am curious to see what happens in MEA2, though. The Initiative is now at war with the kett, so armed vehicles would be appropriate. Perhaps more importantly, many fans wanted a gun. I'm curious to how the new armed Nomads will be, assuming my expectation proves accurate.

I'm curious as to how the Andromeda Initiative will handle defense following ME:A. Assuming you did the H-047c tiller vault, you have a large supply of Helium-3 for fuel but there's still the Kett threat in the near-to-far future plus any other beings that could pop up. Likelihood of the AI developing their own fleet/battleships or do the Angara have such ships?