I was debating about posting these in the General Bugs or Balance Issues threads, but I figured neither place really fit for this subject.
SPOILER ALERT
This topic contains major spoilers. You have been warned.
I have been playing a bit in the single player campaign, and I noticed a few issues.
First, NPCs using bots and batts may make more of a challenge, but there are some things that require you to be able to kill certain ships in a timely fashion.
For example, in M01, when the convoy gets jumped along the way to pittsburgh, there is a way to get an additional bonus for killing off the second wave of rogues. Once the transports jump through, you only have a limited time to accomplish this feat. With the rogues using their bots and batts so much, this task becomes nearly impossible.
Another Example, in M03, there is a point while you're defending Willard Research Station from a group of Rheinlanders where you're instructed to take out a few Gunboats and a small wing of "bombers". Again, you only have a limited amount of time to do this before the cruisers get hit and you take a penalty for failing to protect them. Bots and Batts use here, plus the increased firepower of the gunboats and the second issue I list below, makes this task nearly impossible as well. (Note: I last tested this in 4.81, so it may have changed a bit since then.)
The next issue is the impact of mines. In multiplayer, hitting a dropped mine causes the mine to explode with no real change in ship momentum, as it did in Vanilla. In Singleplayer, hitting the smallest of mines will cause your ship to do somewhere around a full rotation. Although I have not tried this in a freighter or larger, every fighter I have tried suffers from it. Add to that the mine spamming the NPC's are famous for, and you quickly have one very annoyed pilot.
Third, the Connecticut Jump Hole in New York is unlocked from the beginning of the game, making it possible (albeit very hazardous) to explore most of the universe before you're supposed to leave the New York system. The same goes for the other non-vanilla jumpholes in Liberty, once you have access to Colorado, Texas, and California.
Finally, and most interestingly, all non-vanilla factions spend the majority of the campaign neutral. This includes all guard factions, The Wild, and the Admin Faction. Which means once you reach the appropriate levels, you have access to the Admin goodies out on the Lost Battlestar.
While the first issue is relatively mild, and the second is more of an annoyance than anything, the others have the potential to upset the balance in the single player campaign.