Clockwerk is an unfortunate case of a hero who was nerfed too hard, and now scales very poorly in the late game.
When was he Nerfed hard? The last time I see anything major done to him was a string of small nerfs back in 2008:
v6.57: Increased the bounty on Power Cogs a little bit
v6.57: Decreased Clockwerk's Intelligence gain slightly
v6.57: Increased Hookshot manacost from 125 to 150
v6.55: Nerfed the duration on Battery Assault
v6.55: Increased Hookshot cooldown
v6.54: Lowered Clockwerk's strength gain
v6.54: Lowered early damage on Rocket Flare
v6.54: Minor reduction to Clockwerk's base armor
Since then, the only other nerfs he has gotten was his armor reduced by 1 in both 6.64 and 6.72 (But increased in 6.68. Also, it mainly effects his early game, not his late game scaling), and in 6.63 Battery Assault damage reduced being reduced from 20/40/60/80 to 10/30/50/70 (Which is more of an early game nerf, and not a late game one). They did make it so Rocket Flare's Vision doesn't scale, which I guess could be applicable to "Reduce Late Game Scaling".
6.63: Rocket Flare vision reduced from 5/10/15/20 to 10 seconds
Now, for buffs, he has gotten the following though:
v6.60: Added Clockwerk Goblin to Aghanim's Scepter
v6.66: Rocket Flare cooldown decreased from 30/25/20/15 to 20/18/16/14
v6.67: Hookshot Scepter CD from 20 to 15
v6.68: Armor increased by 1
v6.68: Battery Assault damage increased from 10/30/50/70 to 15/35/55/75
v6.68: Hookshot cooldown rescaled from 80/60/40 to 70/55/40
v6.69: Movement speed increased from 310 to 315
v6.74: Power Cogs HP/Mana drain increased from 55/70/85/100 to 60/90/120/150
Did the lower duration of Battery Assault, slightly reduced stat gains, and the nerf to his flares vision completely ruin his late game?