One issue I know of:
Before 3.6.12, the "Secondary Range Multiplier" AI.tbl attribute defaulted to a value based on the index of the AI class. Basically, AI classes higher in the table had lower values and classes further down the table had higher values. The bad news was that Volition designed this hard-coded scaling with only their set of AI classes in mind: as soon as you get more than 12 or so AI classes in the file, the effective "Secondary Range Multiplier" becomes a somewhat ridiculous number, and results in the AI firing missiles from out of range (and often wasting them as a result).
In 3.6.12, this automatic scaling is handled slightly differently: rather than scale between 0 and 9 or so, then get weird as you add more AI classes, the automatic scaling is stretched based on the total number of AI classes.
Really, the best thing to do is to manually set "Secondary Range Multiplier" (and the other AI attributes) to the values you want, rather than to rely on the arcane autoscaling, old or new.
This will affect TBP, since TBP uses a large AI.tbl. Unfortunately, there are probably a bunch of missions that rely on values from the old, fundamentally-broken system. If you want true backwards compatibility, you'll need to go into AI.tbl and set "Secondary Range Multiplier" to values that match the old autoscaling scheme... I can help with the math, if you need it.
If you're willing to let things change a bit, you have a lot of options. My recommendation is probably to manually set the range multiplier to the old autoscaled values, but to cap them at something sane (1.0, 1.25, ex).