For the customisation, none of that generic "replace the main wing actuator to make the plane more agile" or "shove a generic new engine to make the plane faster". Don't put thrust vectoring in every aircraft, ignoring all the structural limitations of each aircraft.
If you want thrust vectoring on a F-5, then they should give us a new version of the aircraft itself (let's call it F-5 Vista). Other than that, just don't do it, I don't want to see overpowered Mig-21 with stealth, thrust vectoring and laser weapons. Complete nonsense.
People speaking about balancing the aircraft: would you like to play gran turismo where the performance of all cars was even? Each aircraft has to have it's strong points and weak points, if it's not that way, we are playing with the same aircraft with just different skin. An A-6 Intruder is supposed to feel heavier, less agile and slower than an F-16.
For aircraft customisation, I would propose this:
F-16A Block 1 > Block 5 > Block 10 > Block 15 > Block 15 MLU (used by many european air forces)
F-16C Block 30 > Block 40 > Block 50 > Block 50+
F-16E Block 60 > F-16V (the new/future variant)
Special versions: F-16 Vista, F-16XL
Each "evolution" would give the aircraft the ability to use new weapons such as the 4AAM (Aim-120 Amraam in this example), that is not available in the first versions of the F-16 (available on the MLU), better radar (which could be seen in terms of the range that you are able to detect the enemy, and/or the lock on range for radar guided weapons). Faster lock ons for standard missiles.
In the case of other fighters which don't have so many variants, you could "evolve" the aircraft through it's main versions (F-15A to C), and then new unlockable variants such as the Silent Eagle, the Strike Eagle and S/MTD.
On the Typhoon side, you could see upgrades by the tranches and respective blocks, with the latest version being more capable than the tranche 1 version.
The other aircrafts would get the same system of course.
For weapon customisation, they could do the same, real life improved versions of each weapon, but this would be problematic, since, for example, the first versions of the Aim-9 Sidewinder weren't that good, and would prove to be kind of worthless.
Instead, just give each aircraft the ability to use weapons that they are able to use in real life, I want an F-16 using a AGM-88 Harm, ECM pods, JSOW, SDB, etc.
And, if possible, the ability to use more than one special weapon. Using different weapon combinations, such as 2 Aim-9 (standard missiles), 2 Aim-120 Amraam and 2 JDAM, on an F-16 for example.
Oh, and also, I would like the F-16 to handle properly statisticaly speaking. In previous games it was pretty much on of the less agile fighters in the game, sometimes being even with tha A-10... Which is not really accurate, since it's almos two times mor agile than a Phantom...