I do agree consolidate is very slow. It rebuilds the VM so it has to read all the data in each VMDK and rewrite it as well as reviewing all the snapshot changes. I am not sure why lab manager would have been faster at this.
One trick we have used in the past to "speed" this up (not fast, but faster) it to have the catalog item in a VDC that does not allow fast provision - and the deploy copies go to a VDCX t hat does (using different datastores and storage profiles). This means the item in the catalog is not linked, and it does take a while for the first spin-up (you would need to test in your environment, but in ours a vapp of that size would take 30 min or so); but the links from this after the first deploy are fast. By doing this - when you place back in the catalog it will have to do a clone operation that is also doing a consolidate - but for some reason it sis much faster.
Maybe Another option - have you looking into using VAAI? If your sotrage vendor supports it you might be able to get vaai clones (on some providers same as linked) - but handled by the storage layer. This can help keep the files a little cleaner.