First thing I would like to say is I haven't read the whole thread as it is getting pretty long so appologies if I say anything that has been said before or make any errors regarding what others have said before me.
Although some of the powers Science characters can use can be pretty annoying for the person being targeted with them you could surely say the same about Tactical characters with the amount of DPS they can deal? Its not so fun having a ship de-cloak and cripple your ship in under a minute either.
There are a good range of counters available to some of the more evil abilities and yes these do take up space on your abilities bar and may force you to spend skill points or BO skill points in an area you didn't want to Science ships also have to defend themselves against other Science ships so it isn't like they have an arsenal of weapons to use against a target but don't have to adequately defend themselves from those same abilities.
I think the game is generally fairly well balanced and I would be interested to hear how nerfing or removing the Science 'super powers' as they are described would actually make the game more fun and balanced? If a Science character or ship doesn't have access to abilities like Tyken's Rift and the like what is it going to have to allow it to compete against Escorts and Cruisers?
I don't want to belittle or insult anyone's opinion like I said I haven't read the whole thread but from my perspective the different characters and ship classes all have their pros and cons and I think on the whole considering the sheer number of different configurations that can exist they are reasonably well balanced.
As for the whole canon arguments do remember that STO is set quite some time after Nemesis, a Tyken's Rift has only been seen in canon once (and another case of one being encountered was referenced in the same episode), years down the line who can say what technological advances could have come to allow a starship to create one itself, looking at the awesome technology available in Star Trek almost any thing is possible and with STO being a game they do have to bend or even break canon here and there to make things work, if they didn't then in every STF I would beam down a legion of Security officers to help me fight the Borg or better yet simply bombard them from orbit