The question about getting wheels other than 2.0 is not clear because I think from what you said earlier the tires you have now are 2.0 inches wide, not the wheel or rim. But to answer, I don't think you need new wheels or rims if you are happy with them (apart from the tires).
For the tires, your only stated criteria appears to be rolling resistance. However I'm guessing you're not racing your 29er on road. You're most likely commuting or something so puncture protection may be important, and with puncture protection weight can be a trade-off. If you state your needs better, it will be easier to answer.
Still, for street commuting and general riding I have used Schwalbe tires on both 26" and 700c wheels, and I've stuck with them because they're so good. I've also done some gentle off-road riding with them, but again I don't know if that is a need for you.
The Schwalbe website rates each of their tires for Speed, Grip, Puncture Protection and Durability http://www.schwalbetires.com/bike_tires/road_tires
I have used the Marathon Plus for years and they are brilliant for puncture resistance, and I feel they are as fast as any MTB slick I've had. I've had one puncture in 30,000km, that was a screw that jacked up into the side-wall whilst cornering. They are however hard to get on and off (I found a good trick on Youtube to do this), and they are heavy.
I recently used the Marathon Dureme on a tour which are a lot lighter than the Marathon Plus and they were fast too, although a bit harder to tell how fast whilst touring.
A 35c width should be faster than a 45c in the same tire, but I switched to a 45c Marathon Plus on the back, from a 35c and I can't tell any difference in speed. The extra volume suits me as I run panniers and so the volume provides cushioning, not only to me but the wheel as well. Again, don't know if this applies to you.
Concerning the fit which you seem concerned about, since you ask if you should get new wheels, I would recommend looking at the ETRTO which is much more standard than traditional measurements which are often mixed imperial and decimal. Schwalbe lists their tires in both measures. You'll see that their 29 x 2.0 inch tires are a 50-622 ETRTO. You probably have 50-622 tires now. The main thing then is that you get a 622 ETRTO tire and that it is not too skinny for the width of your rim. Your rim manufacturer should state a minimum width tire. Make sure you are looking at the same measurement. ETRTO is the most consistent. The 700 x 35c and 700 x 45c you are talking about would be 37-622 ETRTO and 47-622 ETRTO respectively.