I agree Charge Shot seems more useful for default size Gunner, for the neutral B. It really depends on your playstyle and which move you have practiced the most. I recently learned how to B-reverse charge shot, because the input is different than Samus and other B moves, and it can only be done airborne. Figure that one out lol. However I want to talk about side B for a sec.
I think flame pillar is arguably better than missiles, because missiles are just another neutral spacing option, much like fair, charge shot, bomb drop, and grenades. And those are all usually better options than missiles in any given situation. Flame Pillar, on the other hand, is not so useful in neutral but it's godlike for edgeguarding and recovery. Throwing a flame pillar on the ledge while on stage can force the opponent to roll-on in many situations, which is easy to punish. Also, if you jump off and flame pillar backwards so it hits below the ledge, it can automatically stage spike a recovering Ryu, Mario, Cloud, Luigi, Pit, Rosa, and tons of other characters. I've seen Flama doing this recently in his videos. He also uses it to protect the ledge while recovering. Flame Pillar just has so many uses, the angle is unique and surprising, the hitbox lingers and hits below the ledge while on stage, and you can combo off it with Charge Shot or Fair.
Example vid:
https://youtu.be/JdhNWz2tzw4
Scroll to 4:40 and 7:32 and 13:40 (last one is 2 examples, a forced roll-on punish and then a stage spike). Seems like Flame Pillar is literally the most effective move used by Gunner (except for Fair) in this set, and I think it could be even better in the future. (It should be noted that Flama got 5th out of 85 attendees using 1111 Gunner at this recent tournament, which included the best of Mexico. I think you will have trouble finding such results for any other Gunner, even if it was at a regional, and I would be interested to know Flama's opinion of which moveset is best.)
And here's another little vid I made some months back, just to show how much you can abuse this move, often dealing big damage and/or forcing a roll-on. Note how the hitbox is so big, it actually extends below the ledge, and I don't know whether it reaches farther than the ledge-snap range or just consistently 2-frames the ledge grab if timed correctly, but maybe someone else can answer that:
https://youtu.be/rpBKg7cN6RU
I know this opinion is unpopular because missiles are more damaging and easy to use, especially after the patch which reduced endlag, but I have tried both moves a lot and developed my opinion over time. To summarize, everything missiles can do is more easily and effectively done with Fair or Charge Shot in my opinion, both in neutral and while comboing; and Flame Pillar is more useful once you practice the spacing/timing and use it strategically during edge play. If I didn't have flame pillar, I'd be stuck with the same ledge options as every other low tier character, and with missiles I'd simply have another predictable slow-ish mediocre projectile, like we need more of those. I rarely use missiles unless I get bored with fair or don't feel like charging up neutral B.. I just love the sound a launching missile makes but that's about it xD