I'll put it this way: I agree with the general sentiment. Most "temples" don't actually seem at all like holy places, but rather like secret troves for ancient treasures that one would expect to access through passages hidden within said holy places.
The obvious answer to this would be to have "temples" start off as public holy places, with your task for entering the "dungeon" being to find the secret entrance hidden inside it somewhere. Of course, for this to be the case for every dungeon would be repetitive and predictable, so the other obvious solution would be to stop making "dungeon" areas "temples," and instead add more varied things like tombs, secret laboratories, industrial sites, underground passages, outdoor areas, etc.
TP only had three actual temples anyway, the Forest Temple, the Lakebed Temple, and the Temple of Time. The rest were a mine, a city, a palace, ruins, and whatever Arbiter's Grounds actually is...
Realistic dungeons... To some extent, I think it would be good. Like what someone said about the hookshot targets, it is a little odd having targets laid around. It would be good if the puzzles and traps seemed to have a reason to be in the dungeon, other than to wait for Link. Snowpeak Ruins was awesome, the place was like actual ruins, and it has cannons and stuff for defence. Why some of the cannons are inside, and all in all don't seem to have range further than inside the ruins, is a different matter. At least they had a purpose.