What type of speaker would sound better?

ALL other components of the system being equal & IF the room is decent sized I would take a good 3 way floorstander first..

There are many choices… you have to match the flavor of sound that pleases you as well as pick and choose the very best. So, are you spending the same on both? So $5K on mid-tier 3 way or $5K on a high end 2 way? 
 

Assuming careful choice then under these circumstances I would expect the three way to outperform.

But if we are talking about a $2K 3 way and a $5K or more two way… then the 2 way will outperform… it will sound tighter, image better and have a much better cabinet design. It will contain much more design thought and better components. I have heard some breathtaking 2 way high end speakers… leaving nothing wanting.

I will take a high end high performance 2 way over an average less expensive three way any day.    Actually doesn't matter if it's the same price, it's the design ,execution  and parts quality that makes a speaker great.  

I recently bought these , phenomenal speaker

https://www.studio-electric.com/M4.html

One of the best speakers I've owned regardless of size or price.  

There is a myth that many people believe. "If it costs more it must be better." 

Because the speaker is $5k doesn't mean it sounds better.

In fact, there are marketing strategies used to trick the puplic by simply raising the price on an item to change the perception and desirability.

Here is a recent video about the marketing of Grey Goose vodka you may find interesting. Highest price for the affluent crowd that thinks they deserve the best. And the vodka wasn't that good! All a very well done marketing scam. A 2 $billion lie.

https://www.youtube.com/watch?v=npHi2YnLNwI