There is a good wikipedia article with comparisons of torrent client features.
From there, clients that support sequential downloads:
- Shareaza ("available in mod client")
Of those, clients that run on Linux:
Of those, clients with command line support:
- KTorrent ("partial")
- Vuze ("partial")
I'm not sure what "partial" means but that list narrows down your options to either KTorrent or Vuze. You'll have to check their command line interface documentation to see if they support the features you need. You may have to e.g. set sequential options via the GUI once if the CLI does not support that as an option (if you find where they store their preferences perhaps you could automate this at install) - but who knows, check the CLI first, it might do everything you need.
All three of qBittorrent, KTorrent, and Vuze support a web interface of some sort as well, so even if they don't have native command line support for what you need, if you can do it through the web then you may be able to write scripts / programs to automate the tasks. In particular qBittorrent and KTorrent both say they have "remote control through web", so if native command line support does fail, those may be the two to look into first as far as automation scripts go. Vuze supports that as well, although you need to install the appropriate plugin.