Option to bypass some missions (paying for skips with empire points)

Who in their right mind would pay 500-1000 EP to skip quests, it would be a waste of development time, impo. The population building quests can be extremely easy, you just have to work on managing your resources, builds(only build what you need) and micro-management to a degree. Some units take up 2 pop, some 3, some cost more, some cost less, spam build a cost efficient unit(cheap and pop filling) alongside your TCs buidling villagers continously and it's relatively simple to achieve. As but one example(using a 1 pop unit), Egypt spears with the champion upgrade are food only, heavily boom food, spam spears alongside vills and most of your focus is on food alone(alongside aging up).

 

The achieve 200 pop in a set time quests are challenge quests & all challenge quests can be skipped without any effect on the civ's questline. You therefore don't have to do them if you don't want to.

Also as t31os states, these quests are fairly easy with practice.

My strategy is to spam caravans for gold, farms for food & make multiple pop 2 cavalry.
Pump out vills, pop 2 cav & caravans and you soon reach a population of 200.
Vills go just on wood, farms & stone for the 4 TC's

Just don't forget the x4 TC's and 24 houses.

 

They're challenges so therefore they're not important, and they're not stopping you from doing anything else.
And the population limit is hard-coded ... so that isn't likely to ever change, besides having an extra large population would nerf every other quest ... so again, aint gonna happen.