I was messing around with my stock antenna and cut it off right after the rubber base. Basically looks like any other short antenna. On the old Proteges you could take the rubber cap off, cut the antenna short and reinstall for a finished look. It didn't work with the Mazda 3 antenna.
I have a 3.5" stubby antenna coming in the mail though. I was just bored till it came.
Perfectly fine on my protege5.
I just got the identical one in for the 3 and I installed it.
I don't listen to the radio much but when I do it doesn't seem to be an issue. If anything I'd say 5-10% reduction over stock?
If you live in the boondocks then a really good antenna may be more critical. In that case, stock is your best bet.
Shorter may not be better but I'm not going back to the stock antenna. I think the CX7 antenna is too long to my eye. Proportion is important and I feel the 3.5 is a nice look. There are even 1" ones that seem too short and are probably not much better than no antenna.
On the other hand, you can always get some FM antenna wire and string it up underneath the headliner and have the roof antenna just for show.