Skipping is certainly a valid choice in response to how the tech works out. The merc fighter is however very expensive for it capabilities. I try no to use it except as a stop gap.
There are 3 somewhat parallel progressions for crafts. The first is normal interceptors like the predator. These are fast, have missile slots, but are quite frail. These are much like normal interceptors in vanilla
The second type is what i term heavy interceptors. The kraken is the first such. Pretty slow but have high hp, Heavy gun slots, no missiles. Intended for tanking fire in a multiple intercept situation.
Third type is ships like the bonny. Comparatively slow, multiple guns but the main feature is there large troop capacity. Much like the skyranger in vanilla.
This mod has a alot of bleed-over since everything has some troop capacity. There are also various utility craft like the pigeon that fill some support role.
Broadly speaking progression is in 4 stages.
First stage: Bonny, first interceptor(hunter-killer?) starting or near starting tech. More or less don't bother unless the bonny bites it.
Second stage:Kraken, Predator. Beginning of diversification and real ability to fight in the air. Still dependent on 3 items from the black market for building. Still probably better off using runt hours else where. And sticking to a chase to landing game.
3rd stage: Further diversification. Craft of this tier can 1v1 fighters and escorts without needing missiles range advantage. Some ships of this stage need fewer types of black market items. Here one can actually start hunting small targets in efficiency and safety. Caution if your craft weapon tech is lagging. Warships are still off the table but anything below gunship is fair game.
4th stage: Ultimate level craft. Black-market no longer involved except for fusion torch clips. These ships are the pinnacle of their types. Fighters are blazing fast, Heavy's are sturdier the the majority of ufos. Transport capacity is a barracks by itself. Fighting warships is possible with multiple interceptors and a heavy to tank. Note that warships will always have range advantage of at least 15km so the tank is absolutely needed.