The answer is going to undoubtedly be "yes" simply because they're different products. But that's not a useful answer -- the better answer is whether or not the differences matter. Unfortunately, without knowing what you consider "important," it's impossible to give a full answer. My recommendation is to give TSM 2.0 a shot and see how you like it.
I used Auctioneer briefly a few years ago but have been using TSM 2.0 since it was released. After doing a bit of research on Auctioneer's modules (that is, since I haven't used it extensively, take this with a grain of salt), it appears that Auctioneer may excel at the following tasks:
- Auctioneer's "Converter" functionality doesn't exist in TSM out-of-the-box.
- Auctioneer's "Arbitrage" functionality doesn't exist in TSM out-of-the-box.
- There is a difference between Auctioneer's "Milling and Prospecting" functionality and TSM's "Destroy Mode": TSM searchers for the cheapest way to obtain a desired material, while Auctioneer searches for materials that can be made for cheap.
For example, in TSM, you'd do a "Destroy Mode" search for, say, "Ink of the Sea," and it will return prices for the different ways of maintaining the ink (buying directly, milling each WotLK herb, milling each MoP herb). In Auctioneer, it would look at the prices for the herbs and determine if milling is profitable. See this thread.
In general, though, TSM does provide more functionality than auctioneer and (in my opinion) is definitely worth trying. It has a (mostly deserved) reputation for requiring more setup than Auctioneer or other programs, but once done, it has some impressive functionality. It also has an active and excellent help forum here, for any more specific questions.