Watch â€˜The Stolen Earth‘ or â€˜End of Time‘ if you want rageâ€¦
There was silly crap in there (most notably glossing over the Doctor holding off the Daleks for hundreds of years) but the examples given are not them:
* he was there for 300 years before the TARDIS returned, and an unknown period after that. This Doctor thought he was the last one, and had already hung on (presumably) much longer than his other incarnations. It was consistent with what happened in The Leisure Hive when Tom Baker was aged 500 years.
* there‘s a long history of evoking companions (and the Master) before/during regeneration, including just last month for McGann â€” but LOL at Rory getting snubbed, then
* over the long years the Doctor no doubt confirmed who he was, that he was protecting the planet, and advised that coming through would re-launch the Time War. The point of the Doctor‘s name is the Timelords wanted to confirm 1) they were pointing at the right universe and 2) it was safe to come out.