I think you should also be able to get much more than 13.5§m in Jan 99.
Probably not by much. I may have had a couple of meh early months, but otherwise I think it was good. So roughly, I may have lost 1-2 months of good funding increases. Worth checking the saves, I guess.
You seem to skip or abort a large number of missions (even 1/3 or 1/2), even those that could be easily doable without much risks but might be somewhat annoying and/or boring
I actually think that I'm doing too many missions. Training forty agents is too much, 20 + base guards should be plenty. And if you have nobody to train doing research-less missions feels unnecessary.
Personally, I find e.g. cyberweb lairs very easy and also great for training melee;
Depends on gear. Cyber? Go nuts. Otherwise, there are some layouts where robots camp above and refuse to come down, can fry your vested agents like nothing. Also closed terrain shenanigans - you can punch it out with better armors, but not with vests, IIRC. Can be annoying, and there's plenty of tedium going forward.
the farms are also very easy and provide great material for reseach - easier by far than other hybrid missions, because none of the enemy units is a 'sniper'.
I have bad flashbacks about dealing with hybrids. The drones can be a bit annoying, unless you're running cyber. Small convoys (new thing?) are easier, no drones. And they have both workers and soldiers. Medium convoys have rocketeers, but they are fairly important captures, I think.
because smoke in XCF causes in principle CHOKE damage (in contrast to vanilla where it would be useless I think).
Smoke blast itself deals no choke damage, you're awarded with exp just for hit. Even more so, for each hit in the area? I think the "sneakiest" one is scanner morale loss. It leads to panic check, trains bravery and awards Tu/Hp stat gain. Mostly for critters, though.
If I'd have to pick one thing I still haven't figured out is how you in mission debriering screen can move on to another bases
Yep, that's custom thing. I intend to share these sometime.
I suppose you shot down the scarab, because the base defense would have been a lengthier thing
Shot down like 4 or 5 syndicate transports. I guess that was it.
Having all the crew (and/or rotating them in and out) and equipment everywhere is seems like a PITA. But I suppose this cannot really be avoided.
Eh, all the micromanaging seems to be less than one medium-sized battle, so no bother. Also, one trick I devised is to save defense loadout as craft loadout, then buy a car and load the load out - the game will offer to buy missing stuff. Manufactured equipment is more troublesome, though - have to load car at manufacturing base and transfer it with all the equipment to target base. True, equipment needs updating over time. But small updates shouldn't feel too annoying.