I believe FTL in Stelaris will probably involve some sort of multi-FTL ships in the future.
Today in the AMA, Wiz's answer to the biggest design regret/disappointment was the current FTL system, largely because it's extremely difficult to balance (and largely why stations currently are/have to be as crud as they are now) but also said the solution wasn't going to be picking one type and cutting the rest.
IMO, the best way to do that would be to make FTL travel dual- or multi-tiered. What I mean by that is that you have a base form of travel (such as a slower, short ranged Warp, or Hyperdrive similar to what we have now) that any ship with an FTL module can use, and then there is a second, ideal form of travel (i.e. (regular)Warp/Wormhole/Hyperdrive(highways)/Jump when you've unlocked it) that now has harsher restrictions as to where they can go and when they can be used, forcing you at times to use your backup means of travel.
For example, Nebulas, which currently just slow down FTL travel, might outright block some or all forms of higher FTL types, meaning anyone who wants to go into one has to use their basic FTL, creating a natural chokepoint that anyone can use regardless of the FTL types in play. Maybe Wormhole travel is limited to when there is a station that is in-system with the fleet; having your network getting destroyed in a war is a more meaningful impairment to rapidly responding to threats, and while you can still do a deep dive into enemy territory, unless there is a construction ship coming soon after, it's going to take a looong time for that fleet to get back home, never mind hit multiple systems. You could have worlds that are off the hyperlane network, or new galactic "geography" that restricts warp or Wormhole travel in an area. You might even allow, as the OP wonders, for an empire to develop the other basic FTL types, so you can have fleets that are suited for certain tasks (like a Wormhole fleet that can jump past that nebula) or areas of the galaxy (like a Warp Fleet that can quickly move between those worlds that are outside the main hyperlane network.)
Having a second universal mode of FTL travel as a default would also give the devs more tools on how to approach defense. The ever-popular multi-system FTL trap that is often offered as a suggestion to make defenses more worthwhile is often dismissed because of how unevenly it could apply to each FTL type- Warp ships would have a pretty even experience with it, but a Wormhole fleet might be pulled out of their network, or a Hyperdrive fleet could be pulled to a system that by a quirk of the map generator is a half dozen or more jumps from where they were heading would, or to one that's only one jump off. On the other hand, if everyone always had an out that can be relied on no matter where they end up, you can allow something like that.
Anyway, those are my thoughts on it.