It isnt the clippers that are getting tougher, its the AI flying them that is better. As a clipper pilot myself I can tell you the situation is actually worse in 2.1 than it was before as the clipper is still, infact increasingly, woefully under shielded, relative to the modules you put in it. I've been losing shields a lot more and a lot quicker than I ever have, and the spec of the ship has not changed.
To let you understand, if you put a clipper together maxed out on shields with 7A shields and 4x A shield boosters thats 52M of modules + you need a bigger powerplant and coupling to make that work, so you are looking at nearer 80M to get those shields and power systems to feed them. By the time you add this to the basic ship its well north of the hundred million mark. So before you fit a gun, tweak a thruster or a sensor or FSD or interdictor you are north of one hundred million credits and that only gives you 551MJ. By the time you have it fully A-Spec decked out warbird Clipper build with gimballed pulse lasers, 551MJ shields, 14DPS, and more than 143 Million credits tied up.
Take a Fer De Lance, spec it similarly with maxxed out shield boosters and generator, full A internals spec Fer De Lance all gimballed pulse lasers 1029MJ shields, 16DPS, 138 Million credits.
Remember that the clipper, because its weapons hardpoint placements being so far spread out, can only run gimballed weapons so its weapons are rendered inert by chaff. By contrast the FDL has much more closely grouped hardpoints and can run fixed or simply deselect the target and run gimballed weapons as fixed to shoot through chaff. The FDL also has a higher pitch rate than the clipper, but drifts more, but can keep a bead on a target better.
So the FDL costs 5Mil less and is a better ship than the clipper - clipper needs a buff not someone complaining that they are too tough. If you cant take out a clipper easily in a Fer De Lance, don't blame the clipper, take a look in the mirror, and go back to pilot school.