Depending on how much AD you have it might be a meaningless difference or a net buff
Base 61 AD plus some runes should give you a 70ish starting AD
Old: 20 + .4 AD = 23,6 damage. Charged increases to 43,6 with no AP
New: 0.32 AD which should give you around 22,4. Charged increases to 44,8 since the charged damage now scales with your total AD
Get Cleaver or Trinity and you should overall do way more damage than before. Also don't forget he gets extra physical damage on his new stun plus it's a 1s stun at all levels
You're ignoring how the skill ranks up. At level 9, he'll have ~84 AD before runes and masteries which is (84)(0.4)=33.6. Right now base Q is 60 + 0.4 bonus AD. That's a significant loss. Itemizing AD doesn't help much here, whether it's 0.4 total AD or 0.4 bonus AD the math is the same when you're talking about items. What muddies things is how the base CD, on-hit CD reduction, and loss of attack speed will factor into the strength of his Q. The crystal zone bonuses muddy things up further. Off the cuff I'd say cumulatively it's a nerf, should be slower at clearing camps and his early game dueling power outside of his crystal zones is definitely worse off.
The extra physical damage on E was taken from his passive. Whether or not it's more damage is build dependent. Factor in Skarner's usual CDR heavy builds but also add the negative of the damage being physical now instead of magic and it's a wash.
Shield strength buff is nice, although definitely he has to dip into a few health items now to make it worthwhile, but going strict armor or MR in defensive items hasn't really been a Skarner thing going back to S3. Cinderhulk + pretty much any health item makes it worthwhile. Movement speed bonus is effectively nerfed because his reduced base movement speed.
I don't see any particular situation where Skarner sees a big increase in damage output. Early game damage nerfed, starting in the mid-game he'll still need Trinity Force to pump out big damage (he already procs it non-stop so making Q even more spammy doesn't help in that regard). Cleaver will be better not necessarily because it'll increase his damage more than it does now, but rather because it seems like he might have an easier time applying the stacking debuff to help out teammates. Doesn't seem like any increases will be due to his base damage. Both Sterak's and Titanic Hydra seem potential good.
Gotta say though...that mana cost reduction on Q is really, really nice. Like...
top lane nice...
Sterak's and Titanic Hydra look great in general. Sterak's on Skarner might be very interesting.