Should I use time machine to migrate from one mac to another?
Solution 1:
I wouldn't recommend a full restore, assuming it's even possible (Apple can sometimes be a bit funky about system releases on new machines). What you should do is a home directory migration, which I believe you can do from your time machine backup with Migration Assistant when you set up the new machine.
What you want to be careful to do to be as seamless as possible is make sure your new user account has the same shortname as your existing one. That should clear up any snafus you might have with migrating Eclipse as well (I think I saw a related issue for Eclipse on Super User that suggested this.)
Solution 2:
The best way to do this is with Apple's Migration Assistant. Plug the Macs into each other with an ethernet cable and launch Migration Assistant on both. Follow the instructions on screen.
I've migrated to new machines seven times and it's a pretty flawless system. Based on other answers I'm pretty sure that Eclipse won't really know the difference after migration as long as your short name on both Macs is the same.