My gut instinct is you may be worrying too much about graphs that, from what you provide, both are pretty good scans.
I'm a novice compared to many here in reading the graphs, but my take is that the Plextor's jitter values stay much lower (Even with the jumps) than many of the Asus scans. Similarly, the beta value jumps around but stays close to 0 whereas the Asus is a straighter line but farther away. (or am I missing something that the scale in red is irrelevant) The jumps, in general, aren't that severe.
What throws a monkey wrench in the whole thing is it looks like the media on each scan is different! you need to burn the SAME discs, preferably from the SAME spindle, at the same speed/settings/etc and then scan. What type of media was the 'Plextor 1' scan from? (Plextools seems to not like to put bitset DVD+R media codes on scans)
And of course, a PlexTools graph only states how that one drive reads that one disc. As you say, the Plextor discs are working fine. It's quite possible for the media that you buy, the Asus IS a better burner. Don't treat media like it's all equal, because it's not. As someone else stated, the Plextor definitely likes +R media better and Pioneer/Asus likes DVD-R better.
Please post scans using high quality media burned similar ways in both drives for a better comparison of what's going on. (like try using MCC03 DVD-R and MCC04 DVD+R. Ritek and Prodisc aren't the best media for testing..)
My gut instinct is you're worrying too much, you have 2 excellent burners, and the Plextor gives you the ability to do media scans and the like. I have a 716 I use for DVD ripping, DVD+R burning, and scanning. If I want to burn DVD-R or DVD-RAM, I use my LG 4167. Just like with anything, you need to use the proper tools to get the job done.