Yes, indeed, the NMM isn't exactly the first tool of choice for modding this aged game. Primary problem being many Oblivion mods have been packaged in totally alien to the manager folder structures and packaging formats, which the NMM now cannot automatically understand.
- BAIN-ready packaging for installation through Wrye Bash's BAIN? No way the NMM will ever be able to read these correctly.
- OMOD-ready packages or even OMODs themselves for use within the Oblivion Mod Manager (OBMM)? Hell, no, OMODs will crash the tool, and OMOD-ready mods will do the same, when they include a folder called "omod conversion data", which OBMM uses to create an OMOD out of it without any further interaction with you. NMM is based on FOMM (Fallout Mod Manager), at least in part, which uses FOMOD scripts for guided installs. The very second it stumbles upon an OMOD function inside an OMOD script, it will complain it's not a known FOMOD function and just die inevitably.
However, I myself up to now managed quite sufficiently to install and manage every single mod in my now heavily modded (Bevilex' mod list + Angkor's mod list + my own expansions) game with the NMM exclusively, just because one can.
The only thing I needed to do was dive into every not-traditionally packaged/structured mod and, well, re-structure it first, before adding it "from file" into the NMM.
- Does it have optional or alternative files and folders? Get rid of these by doing a manual install as instructed by the readme, just not into your game folder but into a temporary folder instead, which you later pack up again for import into NMM.
- Is it an OMOD? Convert into ZIP file via OBMM, then extract and do as before (it's a bit more tricky using an OMOD script as your manual install instruction, but it works, in my case anyways).
- Is it OMOD-ready only? Delete the "omod conversion data" folder, then do as before.
- Is it BAIN ready? Well, BAIN's structuring is dead-simple, gladly, so just pick your multiple choices from its numbered folders, and combine all you find within, as each of these contains a complete subset of your data folder, no renaming, moving files around or editing left to be done.
BUT... this topic doesn't seem to be about that quite yet.
You're getting "incomplete" downloads did you say? Or is it only the installation through NMM which returns as "incomplete"? Can you extract the archives fine with the packaging tool of your choice? Or does not even this work, and the files themselves are in fact "incomplete", as in the downloads aborted without notice somewhere half way through, leaving you behind with corrupted archives no software can ever extract?
What mods are you having trouble with exactly? Could you link us to their pages and tell which of the files it was, in case there's multiple?