My assumption is that some, if not all, of these anomolies can be explained by improperly adjusted shift linkage. For those of you with problems, I'd recommend trying to get together with someone with a car with no problem and compare "throws" of the two shifter arms protruding from the transaxle. I removed the entire muffler, so my arms are VERY accessible. In fact, I'm sure the guy behind me can watch me shifting through the license plate "hole".
Anyway, there are two cables. One of them moves the arm through a short arc, approximately fore and aft. The other cable moves this first arm up and down vertically. In other words, gears 1 & 2 are in the same horizontal plane. 3, 4 are in another plane, and 5,6 are in a third plane. (I didn't observe reverse yet.) I don't think it would be too difficult to get some reference measurements from a "good" car and compare these to a car with one or more of the symptoms in this thread. I suspect that one of these two cables may be 1/8" or less out of adjustment and could be easily remedied.