A number of these suggestions are pretty specifically about story details. I'm of the mind that the best story is the one the author tells, so I don't really have any input regarding that kind of thing (although that one about the subject dropping in and out of consciousness would be interesting to see as far as the effect on the memory-path-thing goes).
There's a few things I'd like to see as far as gameplay goes. The series is, pretty clearly, about the story being told- with the interactivity frequently downplayed. However, there are a few little gripes with the way the game plays- bugs, clunky controls, and some oddly-handled minigame segments. The big thing is WASD controls- there's two ways To The Moon played- with arrow keys and the spacebar, or with the mouse. Playing with the mouse, though, was realistically the only option, since you needed to wave it around and find where it turned into a magnifying glass- otherwise you'd have to comb every tile of every level by hand. The ability to use WASD and the mouse in tandem would really smooth out the game's presentation. I was also a little befuddled by the strict grid-adherence bit, but I can see why it'd be more trouble than it'd be worth to have freeform movement- I've had experience trying to map collisions to loads and loads of customized scenery, and it's pretty much a nightmare. A little better pathfinding with the mouse controls would be nice, though- I frequently ended up clicking on one thing only to have Rosalene meander off in a totally different direction (and sometimes into a different room). The zombie-Eva shooter bit at the end was cleverly handled and laugh-out-loud hilarious in spots, but the controls were a bit dodgy. Directional firing with WASD, independent of player position? I fought the controls through that whole segment, really. I can tell there was a lot of effort put into making movement work right, but it could stand to be a little better, as controls frequently broke immersion.
But enough about that- that's all stuff for the Technical subforum, really. At least, I think so. I have terrible luck with sorting out subforums and threads when I first join message boards. There's some other stuff I'd like to say regarding narrative presentation.
One of the frequent criticisms leveled at To The Moon is that Watts and Rosalene's commentary and snarking frequently broke the mood. I'd encourage you (as in, Reives, I guess, because he reads at the forums a lot and will likely see this? I could be wrong, but I'll keep using... what's the term, apostrophe? Whatever it is when you're addressing something that may or may not respond.) to avoid overreacting to that criticism. The relationship between Neil and Eva is clearly pretty important (and if the stinger at the end of TtM is any indication, eventually crucial), and their commentary is both genuinely amusing and subtly critical of the gaming mindset. "Why should we care? We're just here to reach the end!" The BATTLE SCREEN YEAAAAH sequence was especially indicative of that, serving to highlight that This Is Not What This Game Is. Providing some well-balanced contrast to the heartfelt and sometimes sentimental tone of Johnny's story was a great idea. I'd recommend taking the purpose that served into account when writing the next story, though- if it's more intense or lighthearted or somber in tone, you'd want to adjust how to treat the way Neil and Eva (or some other characters?) are presented.
Lastly, some manner of... game-like progression would be useful. To the Moon had very little optional content- mainly in the form of flavor text, easter eggs, or branching paths. Perhaps instead of having exactly five mementos and five units of shield durability per memory, you could have, like, six or seven, with some that are hidden but that provide further context for the events of the story- but aren't strictly necessary to proceed. Maybe have collecting extra mementos (or uh, whatever they're called, the little colored orbs that break the memento shield) or perfect-solving the tile flip puzzles would let you unlock further notes or items or conversations or memories or... you know, something for the player to "do" while experiencing the story. While said experience should always be the focus of the game, and you wouldn't want to distract the player, there are people who just won't have the attention span for a totally linear world.
also maybe make those tile flip puzzles be a little harder than "click the diagonal button to win", like i dunno stick some pointless score multiplier in or have moving bits or whatever, spice up those puzzles
So yeah, that's my two cents on how episode two should go! Ultimately, it's going to come down to the story and how it's presented, but I've got no doubt that it'll be fantastic. Keep up the good work, Reives!
EDIT: Oh, while I'm at it, I should mention that the Freebird Games support page is out of date- says all content is available free of charge, no To the Moon stuff, etc. Not totally sure whether the forum's site feedback board is for the message board site or not.