It really depends on what you're using your Jeep for. No offense to my CJ7, but I couldn't drive that thing every day with the extent of driving I do. That thing is such a handful to drive that I can't even think about talking on the phone while driving, much less tap away on my BlackBerry.
I used to drive a 1987 YJ with the same 4.2L I6 as in my 1986 CJ7 I have now, and even though it was several years ago that I sold the YJ, I can still remember enough to say that the YJ handles and rides much better, and is much more comfortable. If this is a daily driver, I would stick with your 1990 YJ. Your full doors and hard top will fit on no problems by the way.
Also, YJs are not "sissy Jeeps." To tell you the truth, my 87 YJ did a heck of a lot better off-roading than my CJ7, but it did have limited slips in the front and back while my CJ7 has open differentials that will just about get stuck on wet pavement. That will all change in time, though. There are lockers in my CJ7's future.
Now, that said, I am head over heals in love with my CJ7 because it's a true original Jeep classic. I love the noises, smells, and the way it handles, and I definitely love the look of it. But, if I had to get rid of my car (daily driver) and choose between a YJ and CJ, it would have to be a YJ...
1986 Jeep CJ7 4.2L I6 T176 (restoration in progress)
1961 Willys 4x4 Wagon L-226 I6 T90 (restoration also in progress)