Wit,
You're points are absolutely dead-on.

You didn't even mention the WIFI feature, on-premises casino, drvie-in parking, luggage storage, turn-down service with chocolate, the wonderful beds and the fact that one can actually get a decent cheeseburger in the News Cafe. Furthermore, every CRT VIP member gets a free keychain and ball-cap, even if he's not staying at the Presidente.
I have made my dislikes regarding this hotel known: rotten flourescent lighting, hard concrete surfaces which reflect even the tiniest noise and the generally "cold" feeling of the rooms...however, it's still a fine place to stay, and I believe their very reasonable rules and procedures make the hotel safer, more comfortable and quieter. With all due respect to the dashing and handsome Hazel, I don't see any problems with such rules and procedures.
Will I stay at the Presidente the next time i visit San Jose? Fifty-fifty chance either way. I really like the ambience and service at the Sportsmen's Lodge, and I'm curious about the Morazan; the price and location of the latter certainly seem perfect. I am reminded by true veterans around here that before the presidente did all the remodeling, the Morazan was the hotel of choice among many hobbyists, and I'll want to check it out as well.
If hotel rules, chica fees and the like bother you, there are numerous alternatives, including renting a short-term apartment (Rincon de San Jose, Sudamer, Vista Linda, Villa Lakshmi and others).
I am also surprised that many guys here haven't tried the Europa, the Clarion (Amon Plaza), Hotel Gran Via or other "chica-friendly" hotels in el centro.

It seems to me that despite the popularity of the HDR, H. Presidente and SL, we have many options in downtown San Jose... and I haven't even mentioned all of the hotels which accept "guests."