Thanks for all the input, now for a few more questions of my own:
I know certain pokemon may very well counter my lead Milotic, but won't every single pokemon I lead with have a potential counter? I'm not trying to say you're wrong, but I feel like my lead isn't my problem, my glaring weakness to Raikou is.
As I said in my previous post, Milotic is a good lead, but in this team context you might want to use Suicune instead, and Suicune as a lead is a little tweaky... I would advise Zapdos as a lead because the opponent doesn't really know what sort of Zapdos it will be, and it can set up Light Screen for Skarmory to work better and survive Magneton's Thunderbolt. Also it is a little faster than the likes of Milotic, which isn't a bad thing for a lead.
I completely realized what you're saying in Blissey's moveset; I wasn't thinking at all when I made that set because I should've realized that if Bliss is in fact my only special wall then what good does counter do? I'll switch it for seismic toss. I think I'll take aromatherapy off as well, considering the fact that two of my pokes rely on a status effect to really work to their full potential (Milotic/Heracross).
If that's your plan, try Wish for the potential Heracross set, though if you are going to use Suicune over Milotic, Aromatherapy might be useful for Suicune's Rest.
On to Heracross: I see the necessity for CB, I'll check the moveset on the strategy dex for what to replace swords dance.
If my Weezing is worthless as it is, should I switch it for maybe Donphan? That cover my weakness to spikes and helps out with those pesky Raikous. I'm just afraid of straying too far from a stall team and becoming just a regular balanced team.
I advised the Zapdos over your Weezing in your previous post, you should try that Pokémon out. Donphan does not counter Raikou good enough to be a "counter" and it doesn't have to, either, becuase you now have Seismic Toss on Blissey and that stops it 100%. For the spikes issue, you should try this team a couple of times on NetBattle and see if it's really a problem. See, your team has 1 offensive Pokémon so it won't be able to provide all the staying power and spikes utility a classic stall team has. As already said, you have a different advantage, so it all depends. If they use a team that doesn't even use Spikes, you're in a better advantage.
Starmie is also a Rapid Spinner so you could try and make a bulky water out of it with something like Recover, Rapid Spin, Surf and Ice Beam or Thunderbolt, depending on what your weaknesses are. For this team pick Ice Beam since you have Zapdos for countering Gyarados already and Starmie should then focus on Salamence.
So try to put Zapdos > Weezing with the aforementioned set, and see what your biggest problem is. You might see that Spikes won't wear you down as fast as your Heracross wears down their team if used right. Indeed, try Wish Blissey with Milotic. With Wish, you might even consider SubSkarm in tandem with Light Screen Zapdos!
As you see there are many ways to go with this team.
Let me know what you think, thanks
