with:
- updated/current graphics
- support for keyboard and mouse, not just keyboard
- proper save game anytime anywhere

while retaining:
- two playable characters, one of which can be controlled by computer, so no co-op necessary

and:
- steampunk theme is a plus but not a must

So, are there any?

You could try ''Armed and Dangerous'' from 2004 if I believe ;) Its from Planet Moon Studios who made ''Giants: Citizen Kabuto''.

It has only single player with great funny story. Has a lot of steam-punk-ish elements, though also a lot of fantasy too. It has pc controllable buddies you run around killing enemies with a lot of bizarre and not so bizarre weapons :)

There are a number of new or modernized isometric shooters that you could try (though most don't have the AI buddy).
If you haven't already played them, I the Shadowgrounds games might be a good starting point. :)

Ah, I forgot to mention above, that when I asked about any other games similar to The Chaos Engine, what I meant was one with top-down perspective, not isometric or third-person perspective.

You're asking for way too much, there's no game that has all of those

I think the closest you'll get to a Choas Engine kind of experience with todays games would be from the huge pile of twin-stick-style shooters (alien breed, alien shooter etc) but none that I can think of comes anywhere close to being similar to CE.