I'm working on a new character in Skyrim and I want to plan ahead for reaching the armor cap. I intend to use Ebony Armor with maxed heavy Armor, Smithing and Enchanting at the very least.

I'm trying to settle on if I'm going 2 handed or sword/board and if I should include Flesh spells. Can Someone give me some insight?

I think flesh spells are unnecessary once you have good armor. As for two-handed vs. sword&board, it's a matter of preference - the former lets you deal more damage, the latter gives you more effective blocking, some protection from arrows/spells and bash.

My character started off as a dual-wielding warrior, but recently I've also been trying my hand at sword&board. When facing a tougher enemy, like a dwarven centurion, I still switch to 2h - a few hits and the enemy's down.
I recommend that at the beginning of the game, you try out a bit of both styles and see what suits you more. It's possible that you'll find both skills useful depending on the type of enemy/type of location. In this case, nothing is preventing you from investing in both perk trees.

If you max Heavy Armor and Enchanting, and get the relevant perk in Smithing you should have no problem reaching armor cap, even without a shield.

My advice is to max enchanting (the five base perks, and then go up the middle of the tree is what I do, the left and right branches don't really seem that valuable to me), get the smithing perk you need, and then start tempering your armor. After you've done that, start taking perks in Heavy Armor, and see how many you need to reach armor cap (you certainly won't need all five of the base ones, and may not even need one if you go down this path).

That way you don't waste perk points going above and beyond the armor cap.

As for fighting style, I loathe sword and board AND two handed, I have much more fun with spellswords and dual wielding.