I'll vouch for St1ckBuG on this (like he needs it; he'll probably just tell me to EAD :x ): I've helped run tournaments at NEC before, and there's a reason the side tournament is always run first: if you run the side event before the main event, people will still generally get their ass up for the main event. However, doing the main event first and then the side event and people would just flake out hard, not getting up on time or deciding to spend three hours at Denny's or WaWa or whatever, or just having to leave early. I know from experience that for stuff like MB and Arcana, teams on Saturday and singles on Sunday would work, but the other way around was always a hot mess.
There's no way you could run anything Friday at the Copa even if you wanted to; it was ridiculously packed last year and I imagine that there's going to be even more people this year. It's a great time (and I'm thankful for St1ckBuG for putting it together again this year), but it's not the time to run anything even remotely serious.
As for the single/team split, I always thought that teams was a response to Japan's horrible tournament format, and has no business being run as a main event at a US tournament.