The ISBN Extract plugin should not have issues with memory leaks if you are using the latest versions - it was explicitly rewritten to prevent that issue in v1.3.4. As for "not being accurate" - it is at the mercy of the inputs you give it, it can never replace a human lookup. If publishers decide to put ISBNs for related books at the front of a book there is not a thing the plugin can do about it. However it gets it right more often than not.
Doing metadata lookups in bulk is always a lottery - again the Calibre plugins are at the mercy of whatever the search engine on the website gives them back. A title which is exactly how you want it may cause ambiguity for the website you are querying. A title which is too long and explicit may result in no ideal matches in which case some websites throw back any old garbage as a "best match". I know my own plugins like Goodreads and B&N etc do their best to validate that the author/titles match what you asked for but there will always be corner cases where it cannot be perfect. Having the ISBN is your best chance of a match to suit. Alternatively use the Goodreads Sync plugin to link your books to a Goodreads one and have enabled the option to put the Goodreads ISBN into your book field. Then do the metadata lookup - its an extra step but will almost certainly guarantee you get the right results if you linked to the right book.
If you haven't done so already try using different metadata source plugins, different combinations turned on etc to find the best source for the books you prefer. Don't turn every single one on. For myself I "walk the talk" and only have enabled the B&N, Goodreads and Fantastic Fiction plugins. That way if I find any issues I can push a new version, and they give me back the sort of descriptions, series and covers I prefer. But to each their own.
As for overwriting title/series/authors - well a simple answer to that is to untick those options in the metadata download configuration, so they won't get overwritten. If you are happy with the values from your import then why would you want the values from elsewhere?
Putting 10,000 books in a library is not a trivial exercise if you want that data to have any quality in your library. That is a lifetime worth of reading. Calibre is not a miracle worker, there is no industry standard for book metadata or how websites make data available. Go to a website like LibraryThing and look at the pile of steaming dung their website data contains from allowing data from any source to be given to it with no validation.
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