Verified answer

Assuming they are the same brand and same quality of speaker: probably a little. Most 4" 3-ways are not the best if you are driving them hard. I have a pair of Pioneer Premier 6x9's and 4" in my truck, same series, same brand, and the 4" are pretty lame in comparison to the 6x9's. I should have gone with a pair of 6.5", cut and built out the mounting location. Larger cone area is always better in this situation if the speakers are comparable.

Also, take a look at how and where the speaker is mounted. I had to build out a plate in the door for my 6x9's out of 1/2" MDF because they would not fit properly and I could only get two screws in. That left a gap between the back of the speaker and the door. After the plates went in, the mid-range bass improved considerably.