My friends and I have had this conversation over lunch so many times
Basically we've talked about all of the same thing you guys have mentioned:
The too episodic nature of the storylines
The lack of (lasting) character development
Too much filler - see Transporter Accident eps
The ruining of the Borg
And my biggest personal beef - everything ALWAYS works out, just by doing the right thing!!
With these points in mind, what we've come up with is a "covert Ops" type of star trek series. Tell the story of the ppl that do things behind the scenes that make it possible for caption X to do the "right thing" and have it work out. These are the guys that are experimenting and using the cloaking device, the meta-genic weapons. These are the guys that do not work within the constraints of the Prime Directive.
I think you could do some really good stuff with this. Character development, which is sorely lacking on all star trek series, could be really well done - you could have the characters who have no problems with what they need to do to maintain the federation, as well as the character who is reluctantly acting out of a sense of duty. If they really wanna get serious about characters, Paramount might wanna think about stealing some writers away from something like E.R. They're characters are fantastic - engaging, FLAWED and evolving - in short - they are human - not whatever the hell ST has been serving up for years.
This could also explaing why the Borg / cardassians / Klingons / Romulans have never been able to get a decisive win over the Federation.
So, what do you think?