Throughout the years I have been several times to this temple and have seen the progress of cleaning and restoration works, more planned museography, as well as increasingly imaginative marketing and gift shop items. It is a good place to witness the artistic and religious mix of different Japanese historical periods along with the many Hindu remnants found in Buddhism, along peculiarly Chinese and Japanese strands of this religion. In a way, everything is there.
Ultimately, though, Sanjusangendo is one of those shrines that induce awe, respect, and a contemplative experience regardless of religious inclination. You can marvel at the beauty and craft behind all individual statues, the massive, multi-armed Kannon, the temple guardians. If you're lucky and aim for a quiet time (low season, early or late in the day) so as to not find yourself amid a throng of tourists and the babble of several-language organised tours, which can get pretty annoying, you can find a quiet personal spot along the hallway and just watch, let the place work its magic.
The garden areas are plain in comparison with much of what's on display around Kyoto, but they're agreeable to stroll and there's a small, half hidden and picturesque Inari shrine if you feel the need for some Shinto after being in the presence of so many Buddhas.