I think Star Trek really NEEDS the "plot of the weeks". Probably all of the strongest and best episodes Trek has ever produced are single-adventures that are neatly wrapped up at the end of the week. Whereas Trek has always struggled with telling a long, "big" story - let's face it, the Star Trek movies never really captured the feeling of the show, and a large, 10-13 episodes season arc feels nothing but a long, drawn out "movie", that usually falls into the same traps as Trek movies do (action, badguy with a revenge plot of the week, being generally pretty bland etc.)
That being said, I think character arcs absolutely(!) have to be serialized in the modern era of television. You simply can't go back to the sitcom format. So even if the SF plot of the week is different, the effects on the characters not only should, but must carry over from story to story.
Overall, I really like the amount of tying your entire season together with a bigger arc. But that arc should take up only a smaller portion of the overall episode count. It doesn't even have to be a single plot - it can easily be only a larger thematic approach (like ENT 3 was all about the Xindi-conflict and saving Earth, and S4 felt like dealing with the fallout of it, politically, character- and technology-wise, and basically entirely took place on home turf).