Pshew.... I was trying to avoid Walrein and Flygon.
Okay - lots of information here -
As a general rule, you want to try to avoid overlap on the team. With mixed types, it gets a bit complicated, but that's a good general goal. Walrein is a bit iffy - the only thing it gets that's good for the team is a STABbed ice attack. Other than that, it really can't do much of anything that Swampert can't do. Flygon is the one that's the bigger problem, in my opinion (in spite of the fact that it's one of my favorites). It overlaps with Salamence and Swampert and Rhydon - there's pretty much nothing that it can do that at least one of them can't do better.
That said though, there aren't any really bad gaps on your team, so there's nothing that you really need so bad that I'd say to absolutely get rid of one of those two. You could maybe do with a good electric attack to take some of the pressure off of Gardevoir. A bit more fire could be nice. Ghost would be nice. Grass could be good (it's the thing Swampert's most afraid of), but there aren't a whole lot of good grass attacks. You definitely need a couple of fighting attacks, but Rhydon and Salamence can potentially handle those.
So it's not that you need to get rid of either of those two - it's just that there could well be something that'll work better.
Anyway -
For Walrein, I'd tend toward:
Ice Beam
Surf
Rest
and.... here's the other problem with Walrein.... Earthquake? then it's identical to Swampert, only without the STAB. Yawn? Not bad. Body Slam? could work. Actually, with Rest, maybe Snore, so it can do damage while it's asleep. Toxic is also a possibility.
For Flygon:
Man... I have no idea. Honestly. Earthquake is the obvious choice, but you don't really need it. Dragonbreath is.... okay. It's not that powerful, but at least it's stabbed. Hyperbeam is almost always a bad choice - it does a lot of damage on one turn, but then you just sit there and get hit on the next. Solarbeam's actually generally worse, since you sit around and take damage on the turn before you use it, and it's grass type, which a lot of things are resistant to. However, you can at least speed it up to one attack per turn by being in sunny weather - either naturally (which does happen in Ruby) or by using Sunny Day.
Thinking about that.... I'd be at least tempted to set it up as a Sunnybeamer. That is - both Sunny Day and Solarbeam, so it would use Sunny Day first, then each Solarbeam would go off in a single turn instead of a charging turn followed by an attacking turn. It's a fairly limited tactic, since it only really works on things that are weak to grass (ground, rock and water), but it is especially cool on waters, since the Sunny Day lowers the power of water attacks. And since Sunny Day also increases the power of fire attacks, you could put Flamethrower or Fire Blast on it and get something out of that. Then round it out with Earthquake or Crunch or Dragonbreath....
The biggest problem with sunnybeaming, aside from the fact that it's only of limited use, is that if you have to switch in one of your waters while Sunny Day is still running, then it's going to be crippled. It runs for five turns, so that's something to be wary of. Still though... I sort of like the idea of a Flygon Sunnybeamer.....
That'd be:
Sunny Day
Solarbeam
Fire Blast / Flamethrower
Dragonbreath / Earthquake / Crunch
This is more of a novelty set - it's not something I'd suggest for any sort of serious competition. But since you've got other things on the team that can handle all the things that Flygon might handle normally, you might as well do something sort of fun with it.
I'll think about it some more and see if I come up with something else. I've got some errands I have to run right now.....