No Download-Accelerators support & Downloads resume for free users.

I'd love if you could go back to bayfiles, if that's not possible, then jumbofiles could be a good alternative.

I agree jumbofiles is really good :)

I recommend http://animegoon.com/, Hiryuu-Subs uses it, too.

Yeah, DLC could also be used for this. And if you change the url of the DLC link from http:// to dlc:// it can be automatically added to jDownloader by clicking or copying to clipboard without manually downloading the DLC file itself (according to this article http://jdownloader.org/knowledge/wiki/...k-n-load).
DLC could have an additional benefit of making links live longer due to it being encrypted.
Another way of adding links directly to jDownloader is through Click'n'Load 2 that can be either encrypted or plaintext http://jdownloader.org/knowledge/wiki/...ssary/cnl2
However people won't be able to use both of these methods without software like jDownloader which is a trade-off.