Well this is disappointing to hear (but glad it has at least received some attention now). As of 4.9 my scheduler has pretty much ceased to exist as well.
All of my custom tasks (which I have full control over and can "log" to watch what is happening) were emailing me TONS of errors -- basically thread aborting. On the same token, they were trying to fire off as many as 5 times each (and these are all reminder services, BTW, so the few reminders that actually sent before it crashed would send mulitple times, doh!). I ended up creating webservices to expose the functionality I needed and wrote Windows services to run the reminders instead. That solved it.
Bringing that up... I actually talked with Joe Brinkman about this at OpenForce a few weeks ago and his response really wasn't comforting. I asked the question in relation to the "Professional" version that will be coming out soon... basically asked that if I had professional and something like this occurred what would they do. In shortened form he told me they'd identify the module that was causing the issue (which I know to not be the case, it is the core) and then I could take the steps to fix it. I'm sure the actual response will be different when the professional version is out and fully supported, but that didn't really give me warm fuzzies. He also confirmed that the "best" solution for somebody with full control over their portal is to indeed use Windows services to foot the requests and offload it from the portal (makes sense, but doesn't help if you don't have control over the module--ie., core or 3rd party).
As with Rob, Timer mode completely kills my entire portal altogether even if I disable virtually all the tasks (I sat down one day and selectively turned them on one by one -- core only and then my own -- and watched it kill the portal each time). Request mode worked better in previous versions as in it actually worked at all, but now with 4.9 it is pretty much dead in the water. Thank goodness I have full control over everything and can write Windows services to handle my tasks.
I very much look forward to a solution but in the meantime will just continue writing Windows services to handle all the new tasks I come up with.