I have a few questions...
1. Since it doesn't synergize that good, how could I build a Rogue-warrior that could stand toe to toe against a normal 2-handed?
2. Is it possible just to focus on Man-at-Arms (2-handed) and just take Scoundrel to level 1 or 2 for non-dagger perks and sneak?
3. Can you please explain to me, why Backstab damage doesn't compare to a 2-handed warrior?
1. I don't know. Rogue doesn't really lend itself well to toe-to-toe fighting, so using points to be a Rogue just detracts from your stand-up-and-fight ability. Rogue shines, of course, in handicapping others, and taking advantage of their weakness (specifically their back being turned, for backstabs).
2. Of course. That would probably be the best way to do it, and certainly would be the cheapest (in terms of ability points and skill points) way to do it.
3. Backstab damage is good, but it's reliant on circumstance. two-handed weapon damage is not reliant on circumstance, and is therefore more reliable. It's also crazy at higher levels, easily dishing out several thousand damage a turn. If that claim sounds unreasonable, try throwing Oath of Desecration and Haste on Madora, give her a weapon with high base damage (like a sharpened custom two-hander, if you've got nothing better handy) and watch her just murder everything, everywhere. To do very high damage with a backstab character, you need to make sure that your enemies are always - or at least usually - looking at and hitting someone else. But with two Lone Wolf characters, you have fewer things to attract their attention, and while it is absolutely possible to keep behind enemies, it takes action points for movement, while the two-hander uses all their action points for mass murdering.
Please do keep in mind that I firmly believe that you can have fun playing a rogue pair, and I have no doubt that you can overcome the inherent weaknesses of the build. I'm just pointing out what I see as suboptimal; that's not necessarily bad.
