Different approaches for different goals. Let's assume we're comparing at the same price point so that it's apples-to-apples in that respect at least.
2.5 way will typically move more air (play louder and/or have better bass) because more of your money is going into woofers, and you have two motors active down low where you need them the most.
3-way will typically have better mids because a dedicated midrange driver can usually do a better job on the mids than a midwoofer can, and may result in a better transition to the tweeter in the crossover region.
This is an over-generalization of course. There are exceptions and the exceptions can be quite interesting. A single low-bass-only woofer that is relieved of midrange duty may go deeper than two midwoofers. Or perhaps a midwoofer is a better match for a particular tweeter than a smaller dedicated midrange driver would be.
If there was a clear "best" format, everyone would be using it. But instead it's a juggling of tradeoffs. I don't use either one, unless you consider satellites + subs to be a 3-way.
Duke