I am doing a long run of 5.1.17 now with all three DLCs active. Here are my findings:
1. Product customization cannot be turned off when starting using script. I had to set it's level to low and simply not use it. However old-style technology disruption is working.
2. Resource premium for some resources is a number common for all cities. It looks weird and AI has certain problems with this. Is it a bug or a feature? In case of a feature it is kinda weird and unbalanced.
3. You can buy soft/internet technologies from parent company with unlimited premium. For regular techs it is limited by 5x normal price which is also not good.
4. Bug: game crashes when you try to buy obsolete camera phone technology from anyone.
5. Bug: AI friendly merge leads to 30 tech in all fields for buying company.
6. Cannot setup radical R&D in subsidiary. Aggressiveness dialog is empty.
7. What Progect Manager and Programmer skills are for? Will adding a second programmer help?
8. Internet companies can advertize in media of own city only. However AI can add media from other cities.
9. Stock focused companies price drops to zero (old bug, I remember it a couple of years ago. "It never happened before and now again"

10. e-commerce idea is kinda buggy as a whole.
10.1. e-commerce. In a setup where all goods are produced by parent and sold by subsidiary, setting up e-commerce leads to following effects. a) all the prices in subsidiary retailers are set to price agreement. b)the price of this price agreement is set to the same value in all the cities. c)all sales are heading towards zero despite positive rating
10.2. e-commerce. software products without retail sales cannot be advertized. (don't know if it is applied to manufactured goods)
Enough for now. I will continue my run and will report back if I will find something new.
Cheers,
megapolis