What kind of features are we talking about here OP, are we sure we mean engine limitations and not code structure limitations? Are you referring to when they say a change is "non trivial"?
I'll give you the best examples I can recall. During a livestream a lot of suggestions were made concerning new mission types, commodity storage, CQC bots, etc. The response from Mark Allen (I believe that was his name) and Sandro was that they were all excellent ideas, but it was very difficult to code them. Yes, 'non-trivial' was used a remarkable number of times. This is when they announced materials would no longer be needed for engineer upgrades until they could sort out commodity storage.
I got the impression that doing these things wasn't hard, but the existing engine was like a five stack house of cards where the changes needed to be made in the middle row. We keep seeing new bugs appearing in established areas of the code every time they change things and that indicates to me (my opinion only) that COBRA does not support a modular code base. If I change a line of code in the FSD boot up sequence, the GalMap shouldn't develop an issue, sort of thing.
The code is reliant on the engine. Adding a new feature like commodity storage should be relatively easy in a modular code system. New database table, background game code to support it, add UI elements, done. We have AI in the game, but we're told CQC bots are a hard thing to realize. However, if the engine has limitations then adding new features can become quite tricky. This is what it looks like to me, so I'm just asking the question. Is the bottleneck the COBRA engine?
Again, I have no inside knowledge, these are assumptions based on my observations, comments from the devs and previous experience working in the games industry.