I wouldn't say this makes mesons useless, but I would say this does the exact opposite of addressing the ultimate objection about them by turning them into early game weapons.
Early game, it shouldn't be too hard to research down to ~30% stoppage chance for a meson, much like you would research up to visible light or near UV laser wavelength by the time you hit ion. At 30%, a single meson should expect to penetrate 3 and a bit layers of armour - quite reasonable for sending them against targets around the ion tech level, especially if you use large swarms of fighters to deploy a hundred mesons or so. (Three is somewhat light armour, but definitely within the realm that I use for things like carriers and missile ships that I don't intend to be on the front line - the exact sort of target a fighter swarm would prioritize.)
If you want to bump it up and say the enemy is likely to have 5 layers of armour, well, each meson has about a 17% chance to penetrate that much armour. Against a swarm of 100 (not an unreasonable number for someone who prioritizes that strategy; I've done it myself) that's 17 internal hits. Not great, sure, but probably more internal hits per interval than you're getting through other means (at least until you've stripped off the armour). Definitely enough to take down this 5-layer ship fairly quickly (although certainly less quickly than before).
Compare end-game penetration chances. A 7% stoppage chance, into which you've sunk a lot of research points (comparable to getting lasers that will do 168 damage) means that you can expect to penetrate 14 layers of armour. Fourteen is a tiny number of armour layers when you're around gas-core AM drives. That laser itself will penetrate about 20 layers of armour (or 24 if you figure in template overflow) and do 17 points of shock damage (calculated according to the new shock changes) besides.
tl;dr: The armour stoppage change to mesons forces them to be only viable in the ion-MPD age and below.