For my Alpha 40, I have the Evolution Power System which is basically an Evolution .46 engine that comes with a flywheel and a 3-blade prop. The flywheel and prop are supposed to help the engine run more reliably (smoothly) at lower throttle (per the manual). My question is if I remove the flywheel and go to a 2-blade prop, will it increase the power? I don't need the lower speeds (throttle), I'd rather have the power.

A 2-bladed prop is more efficient than a 3-blade, so more engine power will be converted to thrust. But, you need to pick the correct 2 blade prop. Low pitch will result in more pull but less top end speed. Higher pitch will give you more top end speed but less pull (thrust). Pick the combination of pitch and diameter that will allow the engine to reach its top recommended RPM range but not over-rev the engine. The manual should give you acceptable combinations.

Also, an APC prop will generally get you more power from your engine than say a Master Airscrew, TopFlite, or Zinger.

Actually, the reason more people use 2 bladed instead of 3 bladed is cost and selection. Twos are much cheaper than threes, so almost nobody is willing to buy threes to test, so hobby shops don't stock them since they'd rather stock things that are popular and sell.

Picking the perfect prop for your engine AND the plane it's going to pull around isn't simple. There are going to be a number of props that suit the power band that engine puts out. And they also have to suit the drag of the plane you have.

There aren't any rules of thumb that work. What works best is to look around (or ask around) for someone flying your plane with your engine on it who has tested some 2-blades and find out what worked for him.

Next best method is to find what props are recommended. Since your engine is an Evolution, and since the Evolution website doesn't bother to mention props.....

Most 46s spin an 11" prop decently. Most props from 5" to 7" pitch work decently. Go buy any brand of 11x6 prop and try it. If your plane is too fast, buy an 11x5 and compare both props with consecutive flights next time out. When working to choose the better diameter or the better pitch, stick with one brand. Once you've settled on dia/pitch, go buy another brand of that dia/pitch, and compare. Chances are good you won't get that far. Most don't. They realize the perfect prop isn't out there. It isn't.

After you've got some flight time, look around and you'll discover every brand of prop, engine, fuel, servo, TX, RX, tires, etc every where you look. And producing some pretty awesome flights.

BTW, the efficiency deal with 3blades is trumped up. They also have 3 blades instead of 2 producing thrust. Want thrust or efficiency? And how does any modeler measure efficiency after all. The guys flying IMAC aerobatics seem to have a majority flying 3s. And their flight performance is scored..... Most things in our hobby are nowhere close to sound bite simple.

BTW, "if your plane is too fast, then...."

Did I mention that nothing in aeronautics is sound bite simple. An 11x6 will be faster than an 11x5, right. Actually, if the engine isn't powerful enough for the drag of the model you chose, an 11x6 might not be faster enough to look like it. And in fact, top speed isn't really the "fast" that matters. What matters is how fast you plane is in that prop test flight when it's coming in to land. Your engine is going to have an minimum rpm where it idles reliably. Most of us bring the engine to idle to land that model. And the speed at that time matters much, much more than when flat out.

Not simple is it.

A 3 blade will actually help some engines idle slower. (They certainly help some climb stronger and/or faster.) So will less pitch. And blade area helps sometimes. (something you get when you got 3 instead of 2 blades, and something you get with some makes of prop, and.....)

Also, there isn't a particular brand of prop that works best, is most efficient, or "best" in any other category. When you get down into the details of maximizing the performance of any given plane, you'll find that props in the same size from different manufacturers give you different performance in different ways. In very general terms, the APC props are harder for your engine to swing through the air than the same size MAS "S" series props or just about anything else. So we say they load your engine more. If your engine is at its torque sweet spot in flight with the APC prop, then that prop will probably give you the most top speed and since it's a wide bladed prop will probably also accelerate your plane better. But going to the other extreme, the MAS "Scimitar" series props are very narrow and thin, so they load your engine a lot less. So if you're choosing props on the big side of what's acceptable, you will often find that the Scimitar lets the engine get into its happy RPM range in flight and so therefore gives you more top speed and more vertical pull. Getting deeper into it, you may find that experimenting with different brands or even different styles within a single brand becomes a trade off. One prop may accelerate your plane better and pull vertical better while the other gives you more top end speed. Then there are noise considerations, cost, idling characteristics, deceleration, and landing performance to consider as well.
So I'll share a personal anecdote that hopefully makes this all make sense. I fly a Kaos in SPA competitions. I flew it for a long time with a MAS "S" series prop, 10x6 size. I had tried a 10x7, but the performance was horrible because the engine didn't have the torque to get into its peak power RPM in flight. Then a know it all came along and told me I should be flying with an APC prop. So I tried a 10x6 APC and found that the engine RPM was lower in flight, top speed felt very close to the same, but the plane wouldn't pull vertical as well. So I concluded that the APC was loading the engine too much, and I didn't want to go down to a 10x5. So then I tried a MAS Scimitar prop, also in a 10x6. The engine was absolutely screaming in flight, had a bit less top speed and about the same vertical performance as the S series prop did. So I decided to try a Scimitar 10x7. That got the engine RPM back down into its happy place, the plane had better top end speed, and vertical performance was every bit as good as it had been with the 10x6 S series. I then tried an 11x5 Scimitar prop. Top speed was way down but the vertical performance was amazing. The engine RPM was down a bit from the 10x7, but it wasn't lugging like it has with the APC. But then we had a contest on a windy day, and I didn't do well because I didn't have the top speed to power through the wind. So now I'm back to the 10x7 Scimitar. Maybe there's a prop out there that would do better than it does, but I'm happy with what I have and I'm used to the way the plane flies with it.

So all that is to say that prop selection is dependent on a lot of factors including your flying style, what you want out of your plane, your plane's amount of drag, and the torque/horsepower curves of your particular engine. To give you a simple answer to your question, chances are you can get an improvement in top speed if you change your prop as that engine's recommended beginner propeller is on the big side and probably isn't letting the engine turn fast enough to make maximum power. It's a pulling prop which is great for a trainer to be used by beginner pilots, but you can definitely change the flying characteristics of the plane by going to a different prop.