EV stuff: Timid ScarfRotom hits 463.5 (464?) speed in the Rain so 466 is the number you want to aim for. Give Ludicolo 228 Speed EVs instead of 224. Give Kabutops 148 Speed EVs.
Timid ScarfRotom hits 463. So go ahead and change all your EVs back to how they were Charmander.
On Uxie, I'd go Relaxed and change the speed IV to 0 simply because you want to U-turn after the opponents attack as much as possible to get your sweepers in unharmed.
I don't know why you have a defensive Scarf Venu but it's pretty silly to lock yourself into a move that isn't even hitting hard. Just to show you how shit-weak uninvested HP Grounds are...54.1% - 64.1% to Manectric. SHITWEAK. Change your nature to Calm and item to Black Sludge/ Leftovers. You can keep the moveset. 0 Speed Scarf Venu only just outspeeds base 80s also, so yeah just ditch the Scarf.
On Kabutops, your EV spread is just weird. Change it to 112 HP / 252 Atk / 144 Spe Adamant if you are keeping them tuned for Rain. HP gives you a nice LO number, 144 speed for Timid Rotom. Max attack for max attack. Rock Slide is bleh when you need that slot to smash stuff like Toxicroak/ Poliwrath/ Milotic etc. as hard as possible. Seeing as you hate accuracy issues, go with Double-Edge. Recoil isn't an issue as it is not your primary attack. OHKOs Poliwrath blablabla.
Gorebyss is fine.
Ludicolo I would seriously reccomend going Swords Dance because Chansey is stopping 4/6 of your team cold. SD lets Ludi just tear up cores and punishes opponents trying to RainStall you via switching. If you do not want to do this, just change your EVs to 32 HP / 252 SpA / 224 Spe. Chansey isn't common anyway.
Change Regi's spread to 252 HP / 40 Def / 216 SpD. 40 Atk does NOTHING for Shadow Claw. Still 2hkos Missy with rocks and you don't 2hko Rotom either way. The 40 defence will benefit you a whole more simply because Registeel is one of your defensive pivots.
Edit:
The other suggestion I have which just re-arranges your team slightly, and would probably need alot more thinking about than the above *easy* changes... is to move Uxie out of the lead position and put a Qwilfish in the lead slot. This means that Venusaur has to go. I really don't see this affecting your team because Registeel checks/ counters mostly the same 'Mons. Getting rid of Venusaur means no free switch for Moltres and a multitude of others because of your shitlow damage output.
The set I use is:
Qwilfish @ Damp Rock
252HP / 96 Atk / 36 Def / 20 SpD / 104Spe (specific inorite??)
Adamant | Swift Swim
Rain Dance
Spikes
Explosion
Waterfall
Simple lead that will hardly ever fail to put up rain/ give a layer of spikes. I prefer this to leads like Ambipom/ Uxie mostly because of Explosion and I find teams try to play around Qwilfish allowing ample Spikes opportunity. The fact that Qwilfish has Swift Swim is just a bonus.
252HP + 20SpD lets you survive an unboosted Timid Max SpA Earth Power from Omastar (quickspikes lead) so against Omastar you have the security of ALWAYS outspeeding, putting down a layer of spikes, surviving whatever attack they use and then being able to Rain Dance. Best bet is to then switch to Ludicolo.
252HP + 36Def lets you survive an EQ from Pinsir allowing you to RD -> Explode/Spike/Waterfall. This is the strongest physical attack that you are actually capable of surviving without a MASSIVE defensive investment. You have Rhyperior to handle Ambipom.
104 Spe lets you outspeed max Omastar, Uxie and whatever else is around that mark. Also outspeeds Scarf rotom.
Rest (96 Atk) goes into attack for OOMPH on Explosion and Waterfall. You OHKO 252/200 Calm Milotic which is nice.
Now that you have Spikes you might not feel the need to have Stealth Rock on Uxie, if this is the case... use Yawn. U-Turn + Yawn is awesome for obvious reasons.