6th Gen Soar vs. Fly...

[Sheep]

Soaring's a feature available later into the games that allow you to ride on Latios or Latias' back at will with the use of the Eon Flute - a lot of people stopped using the Fly HM once this ability was unlocked. It's convenient since you don't need a Pokémon with Fly in your party since Latios/Latias can be called via the Eon Flute anytime even if they're in your PC box. What do you prefer to use?

When flying I want to get somewhere quickly.. and soaring has a longer animation so I tend to ignore it 95% of the time. It's fun seeing the entire region from the sky but the size being so small makes it severely underwhelming for me, haha. So I always have a flyer in my party.

 

[Otamajakushi]

I soar 100% of the time. It's convenient, and I don't need to teach fly to a Pokemon. It's second-nature to me now. I can get anywhere on the map fairly quickly.

 

[Hikamaru]

I used Fly until I got the Eon Flute. After that, it was pretty much just riding on Latias everywhere plus it's also cool you get a nice view of Hoenn from the air and the graphics were so beautifully rendered there. Another benefit of soaring is the ability to catch rare Pokemon on the Mirage Spots and also encounter various legendary Pokemon.

 

[Oblox]

I love soar but I still find myself using fly a lot because it is quicker. I have Fly on my breeding Volcarona which I keep in my party alongside my doubles team so its no issue really.

 

[DarkSkys]

Soar, 95% of the time. 5% went to actually flying.

 

[Drayton]

Soaring - because I might want to stop at any route instead of towns/cities, the battling with flying pokemon up in the sky. But the animation makes it bit delay

Fly (5%) - Just for a quick stop at Pokemon center and save time.

 

[DraconianWing]

Definitely Fly, bar searching for Mirage spots. The Soar cut scene in my opinion takes too long combined with the actual navigation, making it pointless when all you really want to do is to get to another town or city.

 

[Pendraflare]

When I don't have Fly, I just stick with soaring. Really, it's nothing that I think too much about, and I do like the scenery in soaring at least, that's a nice bonus. Also, HOW THE HECK can your Pokémon fight on those clouds if they're not capable of floating?!

 

[Sopheria]

I almost always use Soar. It saves me having to have a Pokemon with Fly with me at all times, plus it lets you dismount at locations other than major cities (like routes or cave entrances). It's a pretty nifty feature and I'm glad they added it to the games!

However, if I do happen to have a Pokemon with Fly on my team, and I'm attempting to fly to a city, I just use Fly. Like Sheep said in the OP, that Soar animation sequence is a bit on the lengthy side.

 

[KetsuekiR]

Definitely soar. I love the tricks that you can do and it's just all around fun! You can also land on every route so that's a big bonus as well!

It's also a good step in the direction of getting rid of HMs for good so yay ~

 

[Tamashi_Seishiro]

I use fly. It's quicker than soar. Soar is for those who want a little adventure in flying. I sometimes use soar, so it's a 50-50 for me.

 

[blue]

I substituted Fly for Soar the moment I got access to it. I find it so much easier to use Soar, better yet it isn't a HM that takes up a move space!

 

[εcho.]

Fly when I have somewhere specific to go. Soar when I just want to wander around and have some fun. The graphics are just stunning and I love just flying in circles over Hoenn.

 

[Starry Windy]

Usually I tend to soar with my Latias because it's awesome that I can wander in the region while going to a certain city or town at the same time, it feels just like in Guardian Signs all over again. However, sometimes I tend to use Fly whenever I want to cut to the chase and going to the destination ASAP.

 

[Sun]

Fly obviously, unless I have no Pokémon that can use the move Fly that time.

 

[Sopheria]

I'm surprised no one's mentioned this yet, but another nice thing about soaring is that it's a convenient way to battle some high level wild Pokemon if you need to do some training. It's pretty nice that you can reach some relatively high level Pokemon (in the mid-forty levels or so) right from any location. Also nice that the wild encounters are easily avoidable if you don't necessarily feel like battling.

 

[Aisu]

Soar! I mean, Nintendo's put so much work into the backgrounds and animation, and as an artist I really appreciate that kind of thing; also, it saves the hassle of teaching a Pokemon Fly/having a Flying-type in your Party. They're handy, I'll admit, but with certain regions they take up space like HM slaves.

 

[Crystal Berry]

I use Fly more often because it's fast, but soar is really nice and I use it from time to time just because it's much more fun than flying.

 

[R2J]

I would say soar, considering I'm also look for new Mirage spots while I was up there.

 

[Dr. Sap]

I almost always use Soar. It saves me having to have a Pokemon with Fly with me at all times, plus it lets you dismount at locations other than major cities (like routes or cave entrances). It's a pretty nifty feature and I'm glad they added it to the games!

However, if I do happen to have a Pokemon with Fly on my team, and I'm attempting to fly to a city, I just use Fly. Like Sheep said in the OP, that Soar animation sequence is a bit on the lengthy side.

It is possible to fly to any route you want, just try selecting somewhere that's not a town the next time you use fly and you'll see that it works ^^

Anyway, I tend to vary which I use. Sometimes it's nice to soar across the world and enjoy the ride to where you're going, while at other times I just want to reach my goal so I use fly. I don't have any pokémon with fly and flame body on my AS so I use soar to get from the daycare to the judge; then it's convenient with soar since I have more room for eggs. However, when doing this I ones spawned on a soaring pokémon and my little slugma was greatly outmatched, luckily I had a Poké Doll to help me escape xD