I have the wooden, the "Take-Along Thomas" and the Trackmaster sets. I like the wooden ones the best.
The "Take-Along Thomas" set is nice for traveling. But, the small plastic tracks can be difficult for little kids to put together without breaking the tabs that fit the tracks together.
The Trackmaster sets are nice too. These plastic tracks are bigger than the "Take-Along Thomas" tracks and easier to put together. However, the trains are battery powered. If your daughter isn't old enough to know that the trains need to be turned off when not in use, then you risk going through lots of batteries fairly quickly. Plus, you can't push these trains around the track manually like you can with the other sets. The wheels don't move unless the trains are turned on.
I like the wooden sets the best. They are easy for little kids to put together and they are durable too. Your daughter can put the tracks together herself however she wants to and in different ways each time. If you buy genuine Thomas the Tank engine tracks and trains, it can get expensive over time. However, any Brio track sets are compatible with each other and can be less expensive. Another nice thing about the wooden sets is that some of the tracks can be flipped over to be used as roads for the small matchbox cars. For your daughter's first train set, I would recommend the wooden "figure 8" set.
I never bothered to get the train table. I think the table is too expensive and limiting. My kids put the tracks together directly on the living room carpet. Sometimes, they come up with very elaborate track designs that would never fit on one of those train tables.
Good luck with your decision. I hope my experience with all three of these different sets have helped you with deciding which to get your daughter.