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Okay so I have decided I'm going to run a command squad with kantor.... It's okay I run a chaplain with vanguard vets so I can take one. I have narrowed it down to either flamers and power weapons or Sormbolters and power weapons..... But what do I choose?!

It depends on the rest of your list. If you're packing a lot of Sternguard, then shooty is less useful, if you're using Honour Guard with Kantor (which is an awesome combo) then maybe more shooting can't hurt.

In a vacuum, though, I'd say 4 plasma and an Apothecary with a drop pod. The shooting can waste most MCs, light-to-medium tanks and anything that pays points for a good armour save.

Ordinarily I would plump for plasma but I want to use either storm bolsters or flamers

Well, both fill the anti-infantry role, so it's really a case of whether you want mid or short ranged; at mid range (Storm Bolters) you'll do less damage, but also be safer from assault, with flamers at short range, you'll do a lot more damage against most targets but find it harder to get into effective range without a Drop Pod and won't be able to make as much use of cover.

Personally, I'd go flamers, as you might as well make use of the high special weapon capacity of the squad.

Unless you really want them, I'd stay away from power weapons; by the time you add them in, you're approaching Honour Guard cost but are twice as fragile and a bigger target.

I struggle to see the value in a command squad. Why they over honor guard?

Since Kantor is locked into using IF tactics, Bolter-based weapons are buffed.
But, why use a command squad? He makes Sternguard scoring, so putting him with them make more sense at first, and Sternguard have nearly as many options.

I often struggle to put cantor into stern guard units. His abilities do not complement theirs. Often times, he will want to drop his bombardment on something other than the target they would like.

Putting him in an honor guard squad gives him more options to crush in HtH while not restricting the shooting of his unit significantly.

Sounds like you've found enough drawbacks to the stock option then.
He is certainly more HtH than the SG.
He's able to leave the squad though, and join them again later.

So, start with what Pedro can do, and fit the squad around him. He's Storm-bolter and PF. I've not used command or honour guard, so I'll see how this turns out.

I just can't imagine NOT using honor guard whenever possible. They are the most efficient HtH unit in the army and unlocking them almost requires they get used!

He doesn't need to be in with them, but it certainly helps to form aa super hard line to prevent enemy units form sweeping your lines.

I want to like stormbolters, but I can’t see paying points for them in this edition. So given that you want to choose between them and flamers, go flamers.

Stormbolters are a bad buy. They're expensive for what they do, you won't do much damage with them, and they're not giving your power swords an extra attack since they're not close combat weapons. Command squads are best deployed like special weapon teams in an IG army. Give them some flamers. Personally I like running Pedro with Sternguard, but that's just me.

I prefer the Honour Guard with Pedro. His basic power armour save and lack of EW means he can't tank wounds, so you really want something with a good save to sort of shield him. His buff bubble is pure HtH goodness, so its a good idea to take advantage of that.