I've been really enjoying my current playthrough of the game with mods. There's only been a few things that have caused me grief (some of which were self-inflicted), however there's one recurring thing that I don't believe has been posted about yet.
When you join a large fleet battle, there are times when your allies clog the area where you would jump into. Normally this is not a big deal as they'll move out within a few seconds - the problem is when the allied admiral AI (or whichever system handles who participates in a in-progress battle) deploys ships with very low CR, or even 0% CR ships. At this point, it is almost guarenteed that the jump area will have ships that cannot do literally anything useful, and when you deploy, you'll go flying at max burn right into their malfunctioning engines.
In a couple instances, I have taken some fairly nasty frontal armor damage forcibly moving the toothless hulks simply so I could participate in the battle. I haven't had any friendly fire incidents occur directly because of this, but I can imagine cases where something squishy, such as a frigate, gets run over by a player's capital ship and dies as a result. To try and solve this, I'd like to suggest two things:
a) that when the battlemap loads up, there's a 'safe zone' where no allied ships will spawn, enabling you to deploy without any problems, and
b) tweaking the joined battle system so ships with 0% CR (or even below 10%) will not be deployed into a battle, since they either cannot contribute at all, or can barely do so.
If anyone needs/wants screenshots of what I mean, I'll try to get a bunch at a later time.