While checking the finances of my different airlines, I was surprised to learn that there's a variable price in the Aircraft family base cost. 

For example, in one of my airlines the base cost for the Bombardier Q-Series Turboprop is $932,143, while in the other it's $888,333. Both airlines are in the same world (S1) and both operates Q300 and Q400 aircrafts in almost the same quantity.

Another difference is of airlines in different worlds (S3A and S1) that operates B747s. In one, the base cost is $7,000,000 and the other a hefty $10,000,000. 

Is that a bug? If not, then why there are those differences in base cost? Why they can be so discrepant?

Ok, so mostly the financial stuff. Thanks for clarifying it, Yuxi. 

Is employee morale affected only by salary or if I have idle aircrafts this will also affect them? Does purchases/sells or aircrafts also affect it? 

In the longer run, purchased aircraft will yield to less cost than if you lease it. The difference is even more considerable if you agree on leases of shorter periods (5 years or less) and own the aircraft for longer time (like 10 years). 

Also, as pointed out by Lord Letto, the aircrafts you own are included in your airline valuation. 

An idea I had, rather than outright bans, was to apply an insane import tax. That way a soviet airline could get a 737, but for the same price they'd get 2-3 TU-154.

You get my vote in this idea. 

Bombardier Q400 NextGen is the answer. 
Excellent fuel efficiency for it's size with best speed in class. Add to this the nice range, reasonable runway requirements and good turn time and you have a win-win aircraft. 
 
The ATRs 72-series are very economical planes too and considering you have an option of smaller plane within the same family and that you can play them for a good part of the game, they're must-have in most airlines. 
 
Best jet-powered plane is the A319NEO, while the B777-300 wins in the wide-body. 
 
And for small aircrafts (45 pax or lower), if only fuel efficiency is considered, than I agree with Lord Letto and the Cessna-Remis F406 wins. However it's maintenance is expensive and unless you have at least 2 of them, in the end of the month you turn red. With this in mind, I'd consider the Cessna C208 Grand Caravan the winner.

If you fly from airports with very high passenger demand (as it's common in Europe, major US and major Asian airports) than you definitely should choose the A380. It has a lower fuel flow x pax than B748, plus it has a higher speed and about 20% less turn time (which becomes crucial in mid to short range destinations). 

However if you intend to use it only on long range flying from/to mid demand destinations, than you should go for Boeing.