Our company is using eclipse since several years now (we are using WTP since release 0.7)
I am currently evaluating eclipse 3.6.2 with WTP 3.2.3 which s
To respond, I'm the lead for the projects that supply the JSP, XML, and JavaScript source editing functionality in WTP. The simple fact is that we don't spend much time on performance tests because we lack resources for doing that. Of course we'd like to be proactive about it rather than reactive, but we tend to allocate our time to functional problems first. We do have an adopter product running performance regression tests regularly, but I expect that tests are run on multi-core machines by now--and we haven't had any new red flags reported to us for some time.
Of the 3 bugs you linked to, 2 predate the 3.0.4 version you laud and the third is either a formatting performance issue (since addressed) or one with as-you-type validation specific to XML files (the fixing of which would have triggered a memory leak in Xerces, iirc, hence us not putting it in at that time). If you have concrete projects that you can attach to a bug and say "doing X is slower in 3.2 by Y amount", we'll do what we can to figure out where there's a regression.
As for the indexers, they should at least eventually complete. The on-disk information that is stored has changed between WTP versions, and those files need to be reprocessed so they're again included in search and (where implemented) refactoring operations. Once the initial indexing is complete, it should act incrementally and be virtually unnoticeable. One architectural change you may be running into is that for JSPs, the entire workspace needs to be indexed in a single workbench session for that index to be considered "up to date". Shutting down Eclipse out of frustration will only prolong the impact of that reprocessing.
It sounds like your company's standard install includes the entirety of WTP rather than rolling your own custom distribution. I urge you to check the Startup and Shutdown preference page and turn off early startup of any functionality you're not interested in using. Nothing you've mentioned interest in makes use of that facility, but there are other areas of WTP and the Platform that do. Anything you're not interested in validating is fair game on the Validation preference page, as well as the setting to validate JSP fragments by default on the Web / JSP Files / Validation preference page.