As far as versatility and overall Thor optimization, Thor/Doom/Doom is more solid than Thor/Dorm/Ammy. If you’ve been contemplating that team, I definitely suggest it. It’s definitely a good thing to look into. Learning Ammy takes a while, though, because she requires a good sense of fundamentals, spacing, and all the stuff that fighting games other than Marvel promote.
As for Doom in general, when choosing which assist to work with, it mostly boils down to the character/team/player you’re fight against. Your playstyle also plays a factor in it, too, but in the spirit of striving to be the best player you can be, a good trait to pick up on is changing your playstyle to better suit the match up. Doom is one of the rare characters in the game that has all three of his assists being good enough to actually work, and also dynamic enough to serve different roles.
Some common things I’ve noticed between picking between Missiles and Plasma:
Missiles is good against characters that like to stay in the air as much as Thor (Zero, Trish, etc). Basically, it’s about giving them something to navigate, something to block, something to keep them grounded or at least honest.
Since Missiles does have long start up, you want to do what you can to protect it. Spark L and/or TK Strike L are what you’ll want to use for it. Also, be smart about when you call it.
When you’re using Missiles in the neutral, your overall playstyle should be a lot more defensive minded when you’re playing Thor. Like a cautiously moving tank. When the missiles have someone in block stun, then you can tri dash L/H to close the distance, but in the mean time, it’s about being mindful about your spacing.
Plasma Beam is better for those characters that don’t care about being in the air, and have the speed to get around on the ground. Basically, your standard rush down characters.
With Plasma in the back, Thor can be a little bit more liberal with his approach. It’s a beam, so as soon as it’s out, the other guy has to stop what they’re doing and block, which gives Thor the time he needs to tri-dash or Mighty Strike in.
Since Doom just gets in and gets out, you don’t have to worry too much at all about when you call the assist. Don’t be silly and call it in those potential happy birthday moments. For that, you need to know how the opponent’s characters normals, range, and speed is.