I have only see Jumboshrimp based in Istanbul(previous gw3),Dubai and Los Angeles which all 3 have large numbers of pax available yes i can fly these bases easy with 2 types too and a 3rd for an fleet transition and not see you in smaller bases which needs more flexability to stay a leading carrier only by a variaty in regional,medium and long haul.
I have been slacking off lately, not really built mega airlines like in the old MT worlds.
But you have to sacrifice something. If you start at an airport that needs Large and Very Large aircraft, you are sacrificing the ability to have a medium aircraft - something that could be very helpful and far more profitable on thinner destinations (if you include staff costs in your calculation, which most people don't).
If you want to fly regional, you may just completely give up on LH, and base at airports that have very limited LH, in order not to attract one of the Mega LH carriers to your airport.
I do agree with one of your points though: the aircraft out of the HQ limit, especially in first 2-3 decades really cripples the concept of regional / super regional. If your HQ at one of the regional type airports only supports, say 50 aircraft, and you only have 200 for out of the base, you are stuck at 250.
In comparison, at airport like LAX, ORD, JFK, LHR, you can get to 400-500 before you even open a first base... So scrapping the limit would open the door for more regionals and for more competition between regionals.
But one word of advice: If you think of a lot of "flexibility" at smaller airports, with multiple fleets of aircraft, there is another thing that can bite you: Base overhead. If you are opening level 3, 4 bases at small airports, that can only support a small number of aircraft, that overhead will kill just as easily as multiple fleet overhead. So you really have to still sacrifice Large and Very Large aircraft in order to be able to open a large number of bases, and stick with Level 2 bases.
And if you are using only Medium aircraft, you don't need more than 3 types, so we are back to square 1.