So, is Battle for New York now considered non-canon? You mentioned it was an expansion of the early Goblin arcs before, but it's not in the timeline. (Not that I want to go searching for that game, since it looked like it terrible when it came out. Plus I'd need to find and dust off my old GBA.)
Its my opinion Battle for New York isn't meant to be Ultimate canon. While the character models, story and setting are obviously based on the Ultimate comics, the plot doesn't jive completely with the comics. Its been awhile since I played it, honestly, so I can't point to anything specific, but if I recall correctly it doesn't fit due to the Goblin story somehow. Sorry I can't be more precise. But it doesn't fit, that I'm sure of. Its kind of like the USM cartoon (though admittedly closer in tone and plot). If you're motivated at all I'd say give it a try, you'll probably be able to find it new or used for less than $5, and I for one would love a refresher on it (just to verify my admittedly foggy memory of it).
Also, now that I'm pretty much complete with the Ultimate, Zombie, and Deadpool trades, I'm about to start with the Squadron comics (sigh, my Ultimate comics OCD is a pain sometimes). Any recommendations on big trade paperbacks that collect a bunch of issues?
No big trades, they're all 4-6 issues each. There's Supreme Power Vol. 1-3 which collects the entire 18 issue run of the first series (which is awesome...the rest sucks), then a few spin-offs: Doctor Spectrum, Nighthawk, and Hyperion. Then it became Squadron Supreme and ran for 7 issues... I think this was collected into 2 trades, or maybe just one, you'll be able to find out on Amazon (careful, because the original SS from the 70's was also Squadron Supreme, and don't want to see you accidentally pick up the wrong version of the team when buying trades if you're not interested in the original that crossed over with 616 back in the day--and were in Ultimate Power...or a close facsimile anyway), then there was the Hyperion vs. Nighthawk mini, and then ANOTHER Squadron Supreme 12 issue series (Vol. 2) which was collected into 2 or 3 trades. The only reason these hold any weight on the timeline is because of the Ultimate Power mini and the Supreme Power/Squadron Supreme teams crossing over, as well as Nick Fury (Ultimate) temporarily being banished to the Squadron universe for awhile (even though the timelines don't match up... if I recall correctly its said in SS he was there for 5 years, but in the Ult universe only about a year or less had passed...). Sorry I can't be more exact with the info as I'm not at home and can't look through my trades/single issues to get the precise info, and its been at least 2 or 3 years since these issues came out and I last read them. I'd recommend Wikipedia (search for Supreme Power and Squadron Supreme and it'll list all the series--or the timeline here, though its admittedly tougher with the issues broken up by chronological order) and Amazon for the books available and which issues they contain.
Let me know if you have any other questions, good luck!