I think its a bad idea, because most of the people that will buy Rebellion are previous Sins' players and will probably have it installed, and it might cause balancing issues with other ships, and people that JUST got into the series and dont own Trinity/previous version.
Not only that, I dont know how Trinity works, but I think it should be for people that own Trinity and/or Diplomacy.
(I bought Sins on Impulse before it was Trinity. #swag)
..... . . . . . . Um..... What?... . . . Seriously! What is that absolute nonsense you just spilled all over your post?
So i know Rebellion is a standalone expansion, but am wondering, do you get anything extra if you have Trinity installed along side it?
In answer to your question, no, you don't get anything special by having both Rebellion and Trinity installed on the same computer. However, Trinity does have a certain feel to the game that is distinctly different to Rebellion due to the lack of Titans and other features introduced in Rebellion. I do really enjoy both games and tend to switch between them depending on my mood and what style of play I feel like playing at that time. My friends and I own both as well, so we all tend to jump between Trinity and Rebellion depending on which style of play we feel like playing at a given time. The only thing I have noticed between Trinity and Rebellion is that they both save to the same location and (at least during the beta) the two games sometimes would show saves from both games in their relative load saves screens. As you might guess this caused some confusion because you can't load a Rebellion game in Trinity and vice-versa. Meaning you had to become careful of your save names to make sure not to lose your game saves between sessions. I think they fixed that issue though, but I'm not sure, so time will tell.
And no, having both games installed on the same computer will have zero affect on game balance. While the 2 games do share the same save location. IE C:\Users\Username\AppData\Local\Ironclad Games\Sins of a Solar Empire\Save-(Single/Multi), they both have their own separate dedicated install locations. Hope this helps.