FD is much better as a counterpick than as a starter. It has dramatic effects on so many characters and matchups, so it really is way better as a counterpick, and I think almost all informed PM players probably think so too. Obviously, FD plays fine and doesn't need to be changed.
However, I have something kind of crazy to say about FD, and I hope people give this some thought rather than dismissing it immediately.
Out of the best and most popular legal stages in PM, there are 4 stages that can be defined as "big": FD, Dreamland, Distant Planet, and PS2. These are the biggest stages because FD, Distant Planet, and PS2 are the 3 longest stages by far (in terms of the width of the main platform) and Dreamland is still very long (only slightly shorter in width than Norfair and Lylat, which are much less wide than the other 3 big stages), but Dreamland has super far blastzones, high platforms, and a high ceiling, so it's still massive overall. (Skyworld has big blastzones and ceiling heights as well, but the main platform is so tiny--one of the tiniest of all stages, in fact--so Skyworld is more of a medium stage in comparison to the 4 big stages I just mentioned).
Out of PM's 4 big stages, PS2 is obviously one of the most popular and neutral stages in PM, so every stagelist should contain it. Likewise, Dreamland is more unique than Distant Planet and FD because it has the farthest blastzones and highest ceiling of any stage, so it's a really good inclusion to any stagelist. In order to maintain balance, there absolutely shouldn't be more than 3 big stages in a stagelist. So, assuming that PS2 and Dreamland are in every stagelist, then it comes down to FD and Distant Planet, and most stagelists pick FD. However, I think that Distant Planet is a better choice. Let me explain.
FD has incredibly similar properties to PS2, whereas Distant Planet is way more unique and healthier to PM's metagame:
-The distance between FD's blastzones and the ledges is 161 on both sides, which is incredibly close to PS2's distance of 156. In comparison, Distant Planet's blastzone distances from the ledge are 148 on the left side and 149 on the right (Smashville, as a comparison, is 150 and 151). Distant Planet is very unique by being a very long stage with short blastzones, unlike every single other big stage.
-FD is also very similar to PS2 in that it has a low ceiling. PS2's ceiling is incredibly low (180) and FD's is nearly as low (188), but Distant Planet is more unique because it has a perfectly average ceiling height of 195. (Distant Planet, Smashville, Yoshi's Island Brawl, and Lylat all have ceiling heights of 195, and 195 is both the median and the mean [195.75] of the ceiling heights of all the stages in the bottom two rows of the css). Basically, both FD and PS2 are stages with very low ceilings, Dreamland is a big stage with a very high ceiling, and Distant Planet is a big stage with an average ceiling, making Distant Planet more unique than FD.
-Also, Distant Planet's platform layout is super unique, only being remotely similar to Lylat (which most stagelists omit anyway). Many people see FD as a necessary stage because of tradition and because it has zero platforms, but I think that FD's lack of platforms actually makes it super polarizing (which is why it was made a counterpick in the first place). Green Hill Zone, Norfair, and to a certain extent Smashville do a better job than FD in my opinion because they are only flat and platformless some of the time, rather than dramatically affecting almost every matchup like FD does. Plus, the only other stage that has 4 platforms like Distant Planet is Warioware, and those stages obviously have totally different platform layouts and are super different stages overall.
-Also, Distant Planet has vertical walls, which is great to have since tons of PM characters can do cool **** with walls.
There is no need for redundant stages in PM, especially when there are so many unique stages in the game, and since huge stagelists have historically been a problem in terms of balance and tournaments running late due to stage selection taking forever. FD has incredibly similar properties to PS2, but is a super polarizing stage due to its total lack of platforms. FD is no longer necessary since PM is not Melee and doesn't have a small number of legal stages. Distant Planet is new, PM-exclusive, and brings new stuff to the table, and I think Distant Planet would be healthier for PM's metagame.
In conclusion, I believe that Distant Planet should replace FD in 3.5 stagelists. I hope some TOs consider this possibility and try it out.