I'm currently trying to make a character based on the Dovahkiin in the trailers. I've planned the following perks for him based his abilities/gear/weapons he uses in the trailers:-

http://skyrimcalculator.com/#278133

I wasn't going to give him any magicka at all and at level 81 his magicka/health/stamina would likely be something like - 100/700/300

However I've recently found out that certain perks can directly affect the effectiveness of shouts such as The augmented fire/frost/shock perks affecting the damage of fire, storm and frost shouts for example. Stability can also affect the duration the slow time shout takes effect for and conjuration perks can affect the newer summoning based shouts like soul tear and Durnehviir. Quiet casting also apparently makes shouts silent which is strange.

Problem is I don't have any perks left to put into these unless I perhaps remove perks from the 2 handed tree which, to be honest, may be a realistic option because I haven't seen the dovahkiin use 2 handed weapons in any of the trailers yet besides the hearthfire trailer where he carries one on his back. Plus most of the really interesting weapons in the game are one handed I think.

What I'm wondering though is was this a mistake/glitch made by bethesda or was it intentionally put in there to affect these shouts? If it is a glitch similar to the vampire necromage scenario then I may not make use of it but if it is intentional then I probably will. It seems a bit strange that it would only affect these specific shouts I've listed and not others like Ice From and Become Ethereal for example. What do you guys think?

Your problems will be solved when 1.9 comes out. The new Legendary skills feature allows you to reset skills back to level 15, allowing you to continue leveling up infinitely, meaning you'll never want for perks again if you want to keep grinding forever.

To answer your question though, I've never found two-handed to be my style so I'd say getting rid of perks from that would be okay.