I have this impression that Henrik Fåhraeus looked at Sword of the Stars and said “This is fantastic, I love how different modes of FTL greatly affect how the races feel and how you play the game. I want to have this in Stellaris”. So they sketch out a skeleton and decide they want Warp, Hyperlanes, and Wormholes as the core methods. They kind of spitball some numbers in there (warp travels X fast, wormholes can transport Y distance) to get something functional in place.
Then, as time goes on, they tackle all kinds of other design issues. This is the first time they’ve made a non-historical game, after all, let alone one that’s in space! I’m sure it’s a learning process for all of them. But before they know it, release is only a few months away and there’s a raft of “must have” features still waiting to be implemented. The different FTL types don’t offer anything compelling, but they have indefinite post-release development plans so since what they have is at least functional, they can deal with it as-is and will just have to improve on it in the future.
Unfortunately, I think the issues with the FTL modes touch so many other parts of the game that there was no easy/quick fix. It’s not something that you can just play around with numbers without having serious impacts on other parts of the game. And you might get things to feel great for one or maybe two travel methods, but then #3 comes along and completely blows up the balance you’ve created.
I think they realized they had made a mistake (well, Wiz admitted as much, wishing they had stripped everything out except for Hyperlanes) and that it was going to take a lot more work than they initially thought. He’s mentioned before that it’s a major issue they want to tackle, but it requires a ton of (re)design work and hasn’t fit within the scope of a free update or story pack.
If my assumption is correct and that they finally feel like they have a design worked out for this, I’m extremely interested in what they come up with. I know Wiz has been hesitant to take away someone’s favorite FTL mode in an expansion, but it makes me wonder if they’re going to try to tweak the existing system or if they’re coming up with something entirely different.