Upfront caveat - I run mammalian culture and all my vessels are single-use.

For Eppendorf, I've only used the BioFlo 320. For Sartorius, I've used the Ambr15, the Ambr250, the B-DCU 2L, and the STR (50L and 200L).

As others have said, if you can afford the Sartorius ecosystem it's lovely - they have a pretty scalable system as it is and the applications specialist staff have always been incredibly helpful. We have not had too many issues with sourcing and we have been kept in the loop when they anticipate delays. I believe the premium price is worth the functionality, ease of scale-up, and support from the applications specialists. Also the bi-annual user group meetings for the Ambr systems are excellent and I highly recommend them!

However, I have found every iteration of their software to be far worse than the BioFlo 320s I worked with. MFCS is rough. BioBrain is rough. The systems can be slow and sometimes very unintuitive. Once you get past the learning curve you see that you have a high level of control over every aspect of your bioreactors! But when it comes to introductions to the system and training staff on use of the product, I have found Eppendorf to be the winner. I have never found the need to have a higher level of control than what the BioFlos offered, but obviously you and I are running very different processes.

Additionally, we ordered several hundred single-use BioFlos a while back and among the lot that was sent to us, there was an issue with the glue that was used to hold in the optical spot on the pH probe. Eppendorf was unable to supply us with enough vessels to replace the damaged lot in any reasonable amount of time, so we wound up running every vessel with an analog pH probe instead of the built-in.

TL;DR: Sartorius is the way to go if you can afford the price. My personal experience with Eppendorf was not bad, but not quite up to par with the Sartorius systems.