One idea that could both nerf spamlining and also adding an interesting element of world progression to larger hubs is to charge an exponentionally growing traffic fee, based on a combination of the proportion of total flights that your airline contributes to, and the total number of flights operating out of that airport divided by the number of runways at that airport (as in all airlines combined). It would obviously ruin spamlining because your individual contribution is exponentionally scaling, but it would also increase the cost of flights at large hubs limited by the runway count, such as Heathrow or San Diego, placing a greater need to run only the most profitable routes out of those flagship airports. Also, since the individual contribution to that cost (your flights / runway count) will be factored into the overall contribution (total flights / runway count), you could feasibly have a huge megaairline struggling to turn profit on a route that a smaller airline could still make money on, since the smaller airline contributes less to the total traffic.
Traffic fee = c1 * (Your airline's flights / Total airport flights)n *(c2 * Total airport flights / number of runways at the airport)
Where c1, c2, and n are variable depending on the size and importance of the airport. Obviously smaller airports would have a lower c1/c2 value, but the n value could be higher since smaller airports would employ less skilled controllers and workers who may struggle to scale when compared to, say, Kennedy Steve.
Also, if runway count becomes a factor, then maybe we could have airlines pool their money to try and expand the number of runways? There could be a system where an airline petitions with the airport authority to build another runway, and the airlines with hubs at that airport can be asked to vote for an expansion. If the vote passes, all airlines at the airport can be asked to make a contribution towards the expansion project by a certain deadline, or contribute more than is required for benefits, such as reduced traffic fees or increased maximum terminal size. Airlines that don't meet this expansion fee will be hit a temporary increase in traffic fees, but this will return to normal in a few months since nobody wants their game to end like this. Obviously this increase in traffic fees will scale based on contribution size v.s. required expansion fee, so if you would be only given a light smack on the wrist if you've made it to 80% of what was needed while you may be priced out of the airport entirely if you didn't contribute anything and are a large presence at the airport. Alternatively, there could be no negative consequences for not meeting the expansion fee, but add a system where the expansion could fail if the airlines collectively don't raise enough money and everyone is stuck with an airport with more demand than supply could satisfy.
Expansion fee = (c3 * (Your airline's flights / Total airport flights))n
Where n obviously also scales on airport size. It would cost more for a larger airport to expand their runways, as they are in more important areas, i.e. adding an additional runway to Heathrow or JFK would be much more expensive than adding an additional runway to, say, middleofnowhereville regional, which is surrounded entirely by farmland. The constant C3 is just there so the expansion actually costs something, maybe it could be a function of total passenger traffic? These expansions should be extremely expensive, so expensive that no single airline should be able to solely fund the expansion, because then it would just promote even further spamlining, wouldn't it?
This method would also mean that airlines with a larger presence at the airport would be required to contribute more towards expansion fees - another way to address the fact that airlines can reach trillion dollar valuations in this game.
I know that AE 4.0 is dead, but I just felt like rambling and you're just gonna have to deal with it.