If anything, this will PROTECT the small guy at the small airport. With aircraft limitations at base airports, why would an airline go to a large airport with a large, strong incumbent carrier for a second/third/fourth base when a medium airport with little or weak competition can handle 100 frames? With unlimited or higher aircraft limits at bases, larger airports become more attractive. This further eliminates the "Fortress" effect of basing at larger airports and will keep strong/large airlines competing with airlines of similar size/strength while leaving the small guy at that medium airport to do his own thing.
If you are calculating the number of planes you can dump to an airport, now every alliance, in theory can dump 200 planes already. And we can see the maximum number of fleet in each base is limited. Some large base, such as CDG, JFK, they can house 400 - 500, that's a huge number compared to 200. However, consider smaller base, like MAN, MUC, PHX, MCO; They can barely house 200 or so. Under the 100 aircraft limit, these bases can be easily fed up by any two players together, preventing others starting in these airport. If the limits is going to lift up to 150, I guess no more base would able to house new airlines after alliance domination.
On the other hand, that means if an alliance is going to attack anyone, that poor airline will have its LF drop to 50% or even lower because his routes is going to be 100% copied, which every big one could fall due to competition, no matter how good you manage your airline. Furthermore, this cause the alliance doing attacking strategy all over the world, because if they aren't attacking others, every moment they are facing risk of BK due to huge competition. I'd guess the situation is even worse than in MT5.