I'm still experimenting on what I should use as Doom's assist and 50Sent's assist.
With Doom Rocks, I can get in quicker and cover more ground and reset pressure quicker. Doom Rocks is great in combos too and mix-up with Zero. When used when the opponent is on the ground in the corner, if they roll they will be stuck blocking Doom rocks and I can attempt a cross-up so they stay in the corner. With this assist, I can keep 800k damage for one meter or pass up 950k with DHC. With 4 meters and X-Factor, I can kill Sentinel. If I do this with Phoenix on a team, I still can lose against certain characters on Level 3.
With Doom missiles, I basically get a "Get outta jail free" assist while pressuring if they somehow hit me. It'll also assist with random supers in a match since it can hit the enemy out of it. Doom missiles also force the opponent to block more and it lasts longer. However, there are some downsides to this assist.
For one, the combo-ability is greatly decreased with this assist. Most likely if I use it, I'll want to use 50Sent drones instead of Rocket Punch as a combo extender. Also, if I land a hit, sometimes the missiles will interrupt the combo which is really bad, and you never know when you will actually hit the opponent. The biggest weakness with this assist is that Doom stays out for a LONG time. People can punish him with a super on reaction with most characters, so I have to make sure I keep him covered.
Right now I'm leaning towards Molecular Shield and Rocket Punch. With Molecular Shield, I can cover the ground enough and just use Zero's command dashes to approach. With Rocket Punch, I can keep combos going like with Phoenix except it also OTGs so that I can combo easier off air-throw. 50Sent Force is good, but I don't think I need it unless I get Doom in the fight, and I usually bring him on tri-jump happy. I'll have to do more testing, it's hardly been a week.