As for tags I don't know the "booru" system (yep :P) but if you think it's a good thing than I'm ok with changing the actual, sometimes not so accurate tags.
But one thing that should be changed/improved/put to debate: the search by pairing tag should search by both "members of the pairing" and not by the actual pairing name - chaotic, but e.g. clicking on "A_x_B" should show series tagged as "A_x_B" and "B_x_A" cause what's the difference? :P (but maybe the actual search result should filter it in two separate groups?) Or in case of pairings there should be only one pairing name tag (less confusion with tagging).
"Sorting things marked by a certain tag by release/upload date."
That would be a very good addition to the search. But how about an additional option to filter things by date/status/"read it"/etc so the results would be filtered with requested colors/markers/order? Or if you want to only tag by release/upload date then add a color/marker/whatever to series that user read/is planning to read/faved/ so to actual result would be more clear?
"Improve connections between the reader and the scanlation groups"
Good thing, don't have an idea how to suggest something interesting that could handle this cause adding additional graphics/buttons/links/etc won't drastically change the major behavior of users that only check the reader and not the group site but maybe you'll figure it out.
Readers choice/Best manga of month/etc could be a fun addition so user can "integrate" more without any social-lame-media?
For Rating systems I mostly find them inaccurate in terms of "this has 9.0" but for me it's like an 6.0 but my 9.0 is "the internet 6.0" so this could potentially lead to users avoiding certain, good series that were poorly scored because someone didn't like the ending so he issued a 1.0. Readers choice/etc is a better way, or displaying the number of favs/views so that users can see what is popular without an actual score.
As for the user having an impact on the tags - maybe adding some "Point System", hidden from everyone but the staff. Each user that suggests a tag that is correct would gain 1 point, the staff could check in some "Top Users" which user is accurate/etc and add him/her to a special "Automatic Approve tags group" so each time that user suggest tags their are added without additional review by staff. Vice versa if a user suggest bad/inaccurate tags or just like to be a troll he "gains" -1 point (or maybe even more for typical trolling) so that each time a "negative" user suggest a tag it is automatically rejected. And with that +/- system user that like to help others will add accurate tags, neutral will stay neutral and "pranks" will be mostly eliminated.
And now my own suggestions (didn't bother to check /u/ topic cause I'm lazy so sorry for eventual doubles):
X Maybe an option to change the default background color of the reader to other one than white?
X An indicator/notice that one of your "followed" series has been updated? (Or maybe this is implemented but I didn't see anything)
X Info on delayed releases - example if group releases something on 1.01 and it's 24h delayed then if you make it visible to the readers after 1 day then add to the name that this release was "delayed" or add it with the actual delayed date (so in this it would be 2.01)
X Maybe an option for the user to customizable their reader front page (like with the blacklist/whitelist/subs/follows, Readers Choice, etc)
Good luck on improving the reader! Cheers.