As Taylor has often said, many if not all limits within FSO will be made dynamic by 3.7, so the ship limit thing won't matter.
In regards to FRED limits, there's a few things I'd like FRED to stop *****ing about. One, is the number of ships per wing. I'm not saying, let it make 12 or something, but FS can handle 6 ships in a wing, it just complains if there are more than 4 in a player wing (Alpha, Beta, Gamma, or custom). Also, it would be nice if it let you select "NONE" as an option for player primaries or secondaries, without a warning message. There's also the thing about starting wing orders. If Alpha wing has orders to do one thing, FRED will complain if Beta wing has different orders.
Another cool option would be (I know, I've said this before) variable density nebulae. Now, this can be accomplished through one of 3 ways, each bringing a greater degree of flexibility to mission design capabilities, but also an increasing load on the coder for the feature. For starters, thanks to objecttypes.tbl, we can designate the fog obscuring distance, but this will affect all nebulae in all missions bound to that objecttypes table file. What I'd like to see, is perhaps a slider in FRED, which adjusts the nebular density within that mission only. The slider would control a multiplier which either increases or the density factor, applied to to all ship classes. For example, if set to 2, all nebular draw distances (even if its going off the hard-coded defaults) would reduce by half, so things would get obscured at half the distance, as number 2 indicates twice the density of the nebula. On the other hand, setting it to 0.1 would mean that the nebula is only a tenth as dense as the default, as applied to all classes. To take it up a notch, if this were to be accompanied by a set-nebular-density sexp, one could set up a series of waypoints, and calculate the player's distance from them at any one point in time, and have it stored in a variable, which would be used to constantly increase or decrease the nebular density depending on where the player is within the nebula. Add to that use of ship-invisible and lightning sexps, and one can create some more sensor obscuring regions. The third level, of this request, would be a more involved system of controlling in-mission nebular density changes, but with something in the background editor, so its more like the often-requested definable parameters to nebulae, making them fully enter and exit capable, without complex events and waypoints. Personally, I thing the 2nd level is at least more easily doable, as the 3rd level would also require significant changes to the background editor interface.