Now, before I start, this is all my personal preference. I have my opinion, you have yours, and that's OK. We all are entitled to our opinion.
OK. I think that Jon is playing guitar live a little too much as of late (since the HAND tour). I mean, there are plenty of songs where it makes sense for him to play guitar (see WDOA and IBTFY), but there are a few where it doesn't. Here's a few moderately played songs in the past few years where Jon uses guitar.
Yellow means that it sounds nice with Jon on guitar but he doesn't need to play it or use a different guitar
Green means that the song should either be played with a different guitar or none at all
Blood on Blood (I think it's much better on electric guitar like in the Bounce promo concerts)
The Radio Saved My Life Tonight (could be much better on electric guitar)
We Weren't Born To Follow (needs no guitar at all; see performance from Giants parking lot and Bradenburg Gate anny,)
These Days (awesome song, but it looks and sounds much better on electric guitar like in the These Days era)
Last Man Standing (another good song, but it just does not make any sense on acoustic guitar, may be better on electric)
Runaway (sweet with guitar, because Jon does a solo at the end, but is just as sweet without guitar like in the early days)
There are many songs when I will hear on the first time and I can decipher just by ear whether he will use acoustic, electric, or no guitar at all. Most of the time I'm right. Sometimes I'm wrong. IMO, using the acoustic guitar kinda takes energy away from the song on certain tracks (eg WWBTF). I just wonder why Jon feels the need to play guitar so much. While some of their most popular songs use guitar, some of them don't (Prayer, Bad Name, Bad Medicine, Always). And when I think about it, very few songs from their past 2 albums don't use Jon's guitar live.
I hope you didn't fall asleep while reading this.
