Ouch. I would argue that TimeQuest is much better for complex designs, and a lot of them would have been impossible with Classic TAN. I think one of the simpler arguments is just the fact that TAN didn't have a report_timing command, so if the path you wanted to look at wasn't the worst case, you had to list thousands or tens of thousands of paths and sort through them. That alone makes me cringe whenever I have to work with the Classic TAN.
But rather than debate it, I'd rather see if there's anything to make your current experience better. Some thoughts:
1) In TimeQuest, use View -> Name Finder. This pops up the window for searching on nets/registers. You can start out with pretty broad wildcards to see what it finds, and then start narrowing it down. (TAN didn't have any special tools for this either, unless you mean right-click locate to Assignment Editor)
2) This concerns me, as I NEVER use write_sdc. Your .sdc file should be a text file that you enter everything into. If you use write_sdc to try and overwrite it, you lose all the niceties of your own syntax, your own comments, your own organization, etc. (And pretty much never use the Constraints pull-down menu in TimeQuest, which would then require you to write out the .sdc file from TimeQuest. Instead, open the .sdc file from TimeQuest's text editor, put the cursor where you want to add a constraint, and go to Edit -> Insert Constraint. You'll have access to the same commands, but under your guidance. (When TimeQuest first came out, Altera was recommending that whole Write SDC flow, and it was a mess. I hated the tool doing that too...)
3) I'm not following the problem. Are you finding registers in the RTL viewer and then making assignments to them?
4) Just because a clock comes in a different pin, doesn't mean it's not related(the DQ clock coming back into the FPGA is a good example.) That being said, I get what you're saying, as TAN's assumptions were right 95% of the time(although the 5% it was wrong caused lots of problems.) Here's what I do once I have clocks in the system(most from derive_pll_clocks). I open TimeQuest and double-click on Report Clocks. I copy all the clock names from the first column and paste them into my .sdc. I then fit them into the following syntax:
set_clock_groups -asynchronous
-group {
}
-group {
}
-group {
}
I then just paste clock groups into each group to get the groupings I want. It takes about 5 mintues and then its done. If there are clocks I'm not sure about(like all the DDR2 clocks created for you) I leave them out so they're related to everything, and then resolve any specific clocks if they show up(but usually they do not). Make sure every line but the last ends with\. You can have as many -groups as you want. A clock can only be in one -group per assignment. Any clocks not in this will be related to all clocks.
I personally think Altera would be in a lot of trouble if they hadn't come out with TimeQuest, and know many users who think it's the number one software advantage for using Altera, so please post any gripes/issues or file SRs. That doesn't mean I don't know users who dislike TimeQuest, as it can be complicated for complicated interfaces, and it's easy to make mistakes(where TAN often hid mistakes and let users continue).