In general, the large publishing houses seem good at exercising poor oversight of their associate editors and providing substandard editorial office service. Accordingly, I'm increasingly interested in publishing elsewhere. Below are a few comments on my experience with some journals, conferences, and preprint servers. Peer review is pretty noisy so these labels of Yes, No, and Maybe may change over time.
YES
MetaRoR- a single experience has been outstanding with critical but fair reviews. Not exactly high-throughput though
Complex Networks and their Applications (CNA)- open to submissions from different subfields. The Proceedings are handled by Springer Nature, which comes with the usual baggage.
Scientometrics- a storied journal that I'll submit to because of so many good articles in it from decades ago.
Zenodo- my preprint server of choice because of the ease of submission and ability to link to Github repos
arXiv- no complaints but appears to be getting overwhelmed
BioRxiv- no complaints
NO
Royal Society Open Science- contradictory and opaque decision making
Scientific Reports- mega journal issues of the usual kind
PLOS One- mega journal issues of the usual kind
Heliyon- mega journal issues of the usual kind
Research Square- just not worth the effort of posting on it
MAYBE
Applied Network Science- both good and bad experiences with things seeming to depend on the handling editor
JASSS- a very knowledgeable editor but individual reviewers can be plaintive and pedantic
Quantitative Science Studies- started on a very promising note but seems to have become inward looking