This topic pops up regularly on the mailing lists, but nothing happened lately.
The OS import tool is still not able to load features with node numbers exceeding the 32bit-unsigned limit, see http://wiki.openstreetmap.org/wiki/64-bit_Identifiers . As a consequence, features get lost, or lines and polygons don't get imported at all, as soon as recently added nodes are involved. This makes the importer quite useless.
Following the discussion here at http://osgeo-org.1560.x6.nabble.com/Suggestion-Remove-Vector-Openstreetmap-tool-from-QGIS-2-12-td5226614.html and on GIS SE http://gis.stackexchange.com/questions/211000/is-there-a-qgis-tool-that-handles-osm-64-bit-identifiers-correctly I suggest to drop the 3-part importer from the Vector menu. Add vector layer and the QuickOSM plugin can import OSM data without the 32-bit limitation.
It would be good to drop the item in the upcoming QGIS 2.18.
Alternatively, somebody would have to change the data type for osm_id in the spatialite export (part 2 of the 3-part-importer) from integer to long integer or text.
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