I could be mistaken but I thought PlanCity included train tracks and accessories. So you could have both worlds in one.
We have a PlanCity play table, and I like the look of it (natural wood) but we have to be really careful about spilling things on it. Obviously we don't let DD eat on the table, but you know kids, sometimes they manage to put food where you don't want them to. Also one day DD had a red wire basket sitting on it, and then spilled water near it, and the red paint kind of came off and stained the table. Sigh. The Thomas table had a smooth finish and therefore you can just wipe it off. But possibly some parents would have concerns about the finish, I don't know.
As for the toys for the table, so far we only have a generic train set (not Thomas or anything) and the PlanCity parking garage. One thing I really like about PlanCity is the cars roll so nicely and smoothly. They are a real pleasure to touch and roll. The parking garage is a lot of fun, but DD can't turn the elevator crank yet (it's large and seemingly suited for an adult's hand, not a chld's... but surely I'm missing something because I'd be surprised if PlanCity didn't test the heck out of that, plus this piece is hardly a new item in their catalog).
Personally, I think I like the PlanCity world best for more opportunities for play, but if my kid had an affinity for trains, I'd definitely get a full train set instead. But with trains, it's almost all about the trains and the tracks. With the City setup, I think it's easier to pretend more things - "let's go to the museum" "let's go to the doctor" "let's play in the park" etc. as well as the vehicle play itself.