The 550 isn't supposed to perform noticeably better in most use cases anyway.
It's running the same execution units and the same eDRAM cache as the 540 in a higher thermal envelope, that's it.
If you aren't pushing CPU and GPU to maximum for a longer time, there won't be a real difference.
As far as I'm concerned, the 13" with TB is a weird in-between product and the worst of all 3 models.
13" with TB vs 13"
- same weight and size
- slightly better performance
- worst battery life of all 3 new models, even compared to the 15" which used to lack behind in this regard
- running hotter
- 300€ more expensive
- TB won't be useful for most people, as a developer I personally prefer function keys anyway
- Touch ID and 2 more Thunderbolt 3 ports are nice, but not worth the other downtrades IMO
I would disagree with most of this, but it's very clearly an opinion which you're more than entitled to.
From a pure features and capability standpoint though, the TB model is objectively better in all performance measures except for battery life.
It's faster in all aspects, including CPU, GPU and wifi.
It incorporates a touch bar and Touch ID, which, regardless of personal preference, is at worst equal to the lower end model, and at best a nice jump forwards.
More Tb3 ports and better internal cooling design.
As for whether this is worth the money, that's entirely up to personal preference and usage.
But I would definitely say this model is still smack dead in the middle of the lineup, like it always has been, between the new "Air" on the lower end and the 15" on the higher end.
For me, the 13" w/TB ticks more boxes than either of the other models. The only thing I really don't like is the price when compared to previous years' models. But that could be said for all 3 models from my perspective