I agree that its a problem, but there is an easy fix for it. Alternate tees!
My home course has par 3s that are nominally 201, 204, 182/199, and 201 yards from the back tees. Prevailing summer winds are cross on two, against on one and with on one, but on a relatively calm day its only a club or two range for me, which is BORING.
However, the first 201 yarder has an alternate tee at 177 yards that's about 20* offset (making the green shallower and more angled, playing more directly over the front bunker and increasing the risk of going into the little pot bunker behind the green for a greater range of pin positions. The 182/199 yarder has two greens (original to the design, along with SEVEN(!) tees, four of which are NLE) and today plays two different tees from the back so it plays from 140-150, 165-185 or 180-200 to the middle, so I may anything from a PW to a 3i on a given day depending on what tee, green and wind I'm facing.
Now most courses aren't going to go to the trouble to construct new greens or seven tees, but there's nothing wrong with alternate tees or just getting a bit more bold and imaginative with moving the markers around so that the tips play next to the regular tees sometimes, or vice versa.
I agree with Tom that par 3s (and reachable 5s) are becoming the only place an architect can force a player to use middle or long irons, so it makes sense to more heavily weight to longer par 3s, at least from the back tees. I'm frankly a bit surprised we don't see 300 yard par 3s, based on the logic that par 3s of over 250 yards were built during the 20s and 30s that required a driver or brassie for a good player. And it would only be fair to see a par 3 now and then that required me to pull out my driver, since my dad is pulling out his more and more often playing from the regular or even in some cases senior tees.