For a start you havnt heard the 2 speakers in the exact same environment, i.e same amp, enclosure, car etc etc as things like Cabin Gain will be completely different from one car to the next and the slightest difference in the set up can vastly improve or decrease the quality/volume of the sound.
But what i think you are refering to is the fact that different speakers sound different is the same set up conditions. This is because of something called TS parameter's.
Look at a similar model to yours.
http://caraudio-bg.com/ts-w307d2.htm
And i presume that you are talking about something like this.
http://caraudiosecurity.com/shop/product/products_id/11431/referer/rc_googleproduct.html
Take things like the X-Max which on the first one is 8mm and the second 12mm (X-max is the maximum excursion of the woofer). So whilst the coil on the second is configured to physically take less power it can travel 1/3 further therefore move more air that is necessary to make sound.
Another example is the sensitivity of the speaker. This is less noticeable in a woofer but on the TS parameters linked above. You will see that the Pioneer is a little more EMO than the JL.
Pioneer 89dB
JL 87.71 dB
So the more sensitive the speaker is, presuming that they have the same surface area then the bigger the box needs to be. So if you put the Pioneer in a strangling sealed Prefab box and the JL in the same then the JL would be more likely to cope and in theory sound louder.
I hope this helps a little. I can possibly explain a little more but i thought that would be some food for thought.
This is where people may get into an argument over the usefulness of Enclosure designing software.
Whilst the software does take into consideration a lot of the TS Parameters and will calculate them a lot better than the average human, there are so many things to consider that often intuition and experience will do the job just as well.
I have never seen a frequency graph from what a computer has calculated, compared to how the actual enclosure performs mapped against the graph of somebody who has made it with knowledge of the ICE world alone. Perhaps i will have a go with mine.