I started playing guitar a couple months ago and have been working diligently on chord changes, pentatonics, bar chords, power chords, and other basics.

I'm 6'3 and have fairly large and stocky hands.

I play an Ibanez RG series with a Wizard II neck. Switching between open chords has been very difficult; I practice the changes daily, but have not made very much progress. Similarly, bar chords cause my hands to cramp and feel unnatural.

I'm not sure if it's simply getting over a newbie learning curve, or the small and flat size of the Ibanez neck makes learning these aspects of guitar difficult.

What guitar necks are good for people with large hands (interested in dark metal, black metal, and prog metal)?

Hand cramps when using Ibanez guitars is probably the most common complaint around here about Ibanez. It's not an unknown of problem.

If you can, try out a ESP or Fender or Schecter neck, something that's a little more average. See how you get on with that. You'll quickly work out if it's the super-thin Ibanez neck that's giving you trouble.
For what it's worth, I have large hands and I love the Ibanez necks, I'd love to go even thinner. I get no hand cramps, though I've been playing for over five years. When I was at your stage I had hand cramps on a much thicker neck, so I would say it's your technique and/or the way your guitar is set up. If your string action is high and you're tensing your hand unnecessarily, cramps will definitely happen.
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I tend to get hand cramps on my Dean's slightly thinner C shaped neck than on my Schecter's more rounded and thicker C shaped neck. I haven't played super thin necks to the point of where my hands start cramping, so I couldn't really say.

You might just want to try out some thicker necked guitars and see how they feel. Schecters, Gibsons, Fenders and Epiphones tend to have thicker necks than Ibanez or LTD guitars.
Thin necks hurt my hands and feel awkward for me. I would say I have medium-large hands. I would say that if the pain doesn't go away after months of playing you need a new guitar.
It's not unheard of to get handcramps while playing smaller necks. It's not incredibly common either. However, I do know that switching to a broader, flatter neck will help in making chord shapes.

I personally like V neck profiles because I find it easier to make barre chords, but I've never found a guitar that I liked in my price range that had one.
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It could be one or more of the following:

1. You're new to guitar and you still need to adjust to it
2. Your posture/grip is straining your hand
3. The action on your guitar, if it's high it will force you to strain harder to fret notes
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I feel your pain, quite literally. I can't do more than a few minutes on a Wizard-II neck. Try a Les Paul or Schecter, they've got thicker necks, fairly think on the electric guitar spectrum.

If you're looking for an excuse to get an Ibanez 7 string, though... the Wizard-7 neck is actually insanely comfortable for me. If I ever got an ERG it'd be one of theirs.
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well it depends. do you want wider? thicker? i mean a les paul baseball neck? or perhaps payattention to the nut width of some guitars. the will specify a wider fretboard.

also, pay attention to hoe the neck feels and its contour. do you think you like a flatter or rounder neck? generally flatter necks are harder for chords and vintage rounder ones feel great for chords.

also, if your hands are actually that big....well hell, a 7 string? i mean your into heavy stuff anyways so eventually in your learning curve you might want the bottom end. plus, 7 strings have HUGE necks.
If you're new to barre chords, you can't overdo em. They tend to cause A LOT of hand tension because most people assume don't have much barre strength and also assume more tension is needed than necessary. I would say, spend a few minutes on tension-heavy stufff like barre chords, take a short rest, then switch to something less demanding like scales, pentatonics, then go back to the heavy stuff. Just don't stay there all night.

A useful primer on how to do barre chords properly can be found here if you need it:

Theres a set of videos on that page by classical guitarist Douglas Niedt explaining proper barring technique. It's not obvious. And when I found those, it help me out a ton.