i think acquiring a company for it's patents is an extremely strong rationale, and that patents should apply universally to all of your assets; after all, this is a real world scenario where IP holders are acquired for their patents all the time. if you're about to purchase a company with a ton of debt and no cash, it's probably an indication that you're about to acquire a ton of deficient workflows that need to be optimized. A cheap acquisition is a tradeoff, you're probably getting a good deal on the assets, patents, and claims , but you'll need to put the time in to scrap the losers and make it run efficiently. 

Strange, I could swear you acquire patents upon buyout.

In fact, I was just playing the scientific tutorial, had a very positive revenue stream, bought out the second to last company, and all of a sudden found myself in a massive water deficit, which, in time with a (random, as there were no hacker arrays out) water shortage led me to bleed $2000 per SECOND. I quickly stopped auto-supplying all of my farms, the primary water consumer up to that point, to no avail.

Turns out I'd just aquired the water-powered patent, and all of my blimps were now sucking down my economy's lifeblood for fuel (whereas I had a nice fuel surplus that they had been using just prior to the acquisition).

Perhaps a recent patch introduced this mechanic?

I can't describe how disappointed I was the first time I bought out a company for the teleportation patent and still the little ships kept flying...

There's definitely a lot that could be done with the buyout/acquisition functionality. It seems strange that I own the HQ, and the buildings, but can't build new buildings of that type. Buying out scientific might be a lot more attractive as another type if I could either build scientific glass factories, or got a combination of the bonuses. I've also noticed that you don't get the adjacency bonus for different types of the same building, e.g. putting an expansive glass factory next to a scientific one doesn't give a bonus.