edit: In the meantime, I have tweaked the rules above in response to feedback and another trial (but only solo) game so the activation rules are no longer as described above.
The other two reasons are in reality equally soft. It really isn't hard to remember which models have activated but it is a bit easier if you do it by squadron (I moved a valkyrie last turn so I'll have to move another this turn). In order to utilize the close formation rule, you pretty much have to activate by squadron as the models all fire simulataneously when using the rule. With my new reserve fire rule, you could theoretically get around that restriction but I wanted to minimize the counters on the tabletop since the main game doesn't use them.
The second bit of feedback was much broader in the form of a question about why the skirmish rules need to exist at all with the introductory scenario rules in the book. The introductory scenarios are very rigid without any structure to expanding beyond what is written. In the first scenario, one side gets 2x VF-1A (40pts) versus 6x Regults (35pts). There is no room for tweaking with the rules as written and the forces aren't even technically equal. They're perfectly adequate for learning the rules which is their primary purpose but not for playing a fuller game at a smaller points total. You could always just say "take whatever you want for the same points total" instead of using my Vermilion rules and that would be perfectly acceptable. I'd like to think that my house rules offer (in 40k terms) a "kill team" set of organized rules as opposed to just playing unbound at 200pts instead (which is what that alternate "take whatever" option would be akin to).
For instance, in the above scenario, a pair of players who picked up a copy of the rulebook at gencon for $10 as well as the two model packs above could either play:
2xVF-1A (40pts) + Long Range missiles (10pts) versus 6x Regults (35pts) + Veteran Warriors (10pts) + Grel (5pts)
Instead of just the two vanilla unequal forces in the intro scenario. My goal was to come up with some skirmish scale rules that would allow folks to pretty much pick up almost any box and be able to play a customizable full feeling game with it versus another. The only exception to this would be if someone bought only a "special" card only box like a Glaug Eldare or Mac II Monster box as specials need to be attached to a support card still due to their intended rarity in game. Another sample force straight from the anime unplayable in the main game:
Sweet Sixteen Attack
versusBotoru Squadron (6x Regult 35pts, 1x Glaug 20pts, 2x Light Artillery Pods 25pts, Khyron 10pts) 90pts
You could expand the above forces with the models that come in their boxes to add in a VF-1S with Roy Fokker for the UEDF and add a second squadron of another 2 artillery pods plus recon and recovery pods (along with veteran warriors) to bump up the skirmish game to the max 150pts.
Which brings me to the final point for this post which is why I set up a limit of 150pts. The first and foremost is that I intended these house rules to be at a specifically different model count than the normal game that starts at 300pts. At 150pts, you could still spam two dozen units on the zentraedi side using stock regults or infantry which is already stretching the goal of a "skirmish" game to the limits. Using the custom RPG character conversion rules, I could easily see the more expensive RPG character models going right up to the minimum 300pt main game limit without increasing the model count. That could be useful for players who want to enact combat scenarios from their RPG campaign with a bit less lethality than the normal game would have.
As always, thanks for reading and feel free to leave feedback in the comments.