1. (It's believed that the feather points to Gilda being the murder because she had a history with Rainbow Dash) Gilda is not involved with this murder.
Reason: It's been shown that the writers are not afraid to use original characters when they have too. For example, Ace Swift is an original character. Meaning that we will meet more original character(s) in the next episode. Also, Gilda would take a more direct route than come up with a plan like this.
2. (It's believed that Trixie is trying to get back at Twilight by framing Rainbow Dash. Also, it's believed that Trixie murdered Ace Swift) Trixie is not involved with this murder.
Reason: Trixie is not a Killer. Killing would result in being caught, and being banished. As you can guess, it would be hard for anyone to see your magical abilities if you are banished to the sun. Also, Trixie wouldn't go about framing someone because it would just be easier to put a pony in jail (banished in this case), then it would be to come up with a complex crime that could result in her being sent to jail (banished in this case).
3. Ace Swift was NOT wearing his electrical protection suit at the time he was murdered.
Reason: Applebloom explains that she was scared by lighting at 8:40pm. The believed time of the murder. Eventually, she comes across some one with fur (She said she felt fur) and they are breathing heavily. Now, what if that was Ace Swift? If that was, then why did Applebloom feel fur? Why didn't she feel the electrical projection suit? That's because he wasn't wearing it at the time. If that's the case, then that means the suit was put on AFTER he was killed.
Also, why would he wear his suit in the first place? It seems odd that he would wear it.
What reason would Ace Swift wear his suit at this time at night, and when he is having a meeting with Rainbow Dash?
4. The blinding light came from a Unicorn.
Reason: Applebloom states she saw light that blinded her and it prevent her from opening up her eyes. Eventually, she was able to, and she was outside the forest. Notice a problem? If it was some creature with wings, then why didn't she mention the wind going across her face when she was in the air, or the fact that she was not touching the ground. Those are things that anypony would remember. Also, why couldn't Applebloom open up her eyes? The reason is that a Unicorn used magic to prevent Applebloom from opening her eyes. The Unicorn teleported Applebloom out of the forest because she had to walked into a murder scene, and Unicorn was not ordered to do anything about Applebloom. Also, she used the light to blind her, so most people would just believe that it was some animal in the forest.
5. The being behind this hates Dash because this being was pranked by her, or it was because the being feared that Rainbow Dash would beat her in the race. Also, the being is trying to get rid of Ace Swift, so the being has a better chance in the race.
Reason: It's clear to me that there has to be another being involved in this case. We know that Rainbow Dash didn't do it, and Ace Swift couldn't have been the one to set off the cloud. For the simple reason that his hoof prints would be on it. Unfortunately, I have no explanation as to why the Cloud wasn't where it was suppose to be. My only guess is that Rainbow Dash was given a fake schedule to move the Cloud over Everfree forest. During so would deliver the weapon WITHOUT anypony drawing attention to it, because all other ponies would just see Rainbow Dash during her job. It seems strange, but Ace Swift was able to get his hooves on some embarrassing pictures of Rainbow Dash. So, maybe he; or someone else, was able to plant the fake schedule.
This doesn't cancel out my theory that a Unicorn was there. It's possible that the Unicorn was hired to kill Ace and frame Rainbow Dash.
6. (It's believed that the metal was a medal) The metal is not a medal.
Reason: Same reason as number 3. Why would anyone wear a medal to a meeting? It just seems odd.
It's like if Rainbow Dash wore her element of loyalty to go meet Ace. However, even though I don't know where the metal came from, I do believe it's where the second lightening bolt went. I believe this to be the case because in this world lightening only makes a noise when it hits the ground. If that is true, then the metal might have absorbed the lightening bolt, and prevent any sound from being produced because the lightening didn't hit the ground.
7. (Guess of what will happen) Scootaloo will lie under oath in order to protect Rainbow Dash.
Reason: Scootaloo is a HUGE fan of Rainbow Dash. Meaning that Scootaloo would not want anything to happen to her, so she will lie to try and protect her. Too bad for her, Phoenix Wright will see right though her testimony.
This will lead to Scootaloo breaking down in tears, she will start to run her mouth. In those rambles, Phoenix Wright would found something that he believes to be vital to the case. Evenutally, this will lead to Rainbow Dash getting off the hook.
8. The second lighting bolt will turn this case on its head.
Reason: Ace Attorney games will usually have something that will cause everything we thought we knew to be false. I believe that the timing of the second lighting bolt plus where it disappeared too will change everything.
9. (The ninth guess is here to bring up an idea that many have. I don't really believe this to be the case.) A Griffon is behind the murder of Ace Swift and the framing of Rainbow Dash.
Reason: We know there is a feather that can't be explained. Most believe it is Gilda, or at least a Griffon behind this. If this is from a Griffon, then why did it fall off the Griffon? My guess is that a Griffon was wearing metal at the time. Let's just say this was a medal. Just like another theory that many people believe. Although, in this case, the Griffon wore it was he/she is very arrogant and wants everyone to know about his/her achievements. Now what happen was that the Griffon set off the cloud (we are assuming that a Griffon can do this at this point) that killed Ace. Then she wiped away her markings. She flew away, but was hit by the lightening coming from the cloud; however, she survived because the medal took most of it. However, some of the lightening still went though, and she lost her feather due to the lightening. Applebloom just happen to found some creature in the forst the glowed, and she left the forest her own. Rainbow Dash left very quickly because she didn't went to be around Ace anymore.
Those are my thoughts. Eight there I believe, and a ninth one that is there to try and follow what some believe. (Although, in some theories, Trixie is involved too). There are some that aren't about what happen, but it's interesting to think about what WILL happen.