Location, location, location! The Jonathon is hands-down the best hotel if you're looking for a place that's within reach of everything in Centro Historico. You can walk to the mercado, Olas Altas beach and the malecon, coffee shops and restaurants, and you're almost literally in Plazuela Machado. The staff are super friendly and always available to help. The hotel used to have a rooftop poolside bar a few years ago, but the neighbors complained. So now the rooftop is a quiet oasis to relax in the lap pool or find a sunny spot on a chaise lounge chair.
The downside to the place is that the breakfasts are not what you'd be familiar with in the US or Canada. There's a small fridge atop the bar with "juices" (nectars), an urn of coffee and sugar-laden pastries (one of each type of variety). So if you normally feast on donuts and pastries for breakfast, that's what you'll get here. If you want a substantial breakfast... eggs, toast, bacon, etc... you'll have to venture out to any one of the several breakfast spots closeby.
Also, on Friday and Saturday nights, it can get quite noisy in Plazuela Machado with load music that can play on until 3:00 am. So if you're looking for peace and quiet on the weekend, the location of the Jonathon might not be your best option.
Aside from that, I've stayed there twice and will continue to do so, unless I'm looking for a house-keeping (i.e. kitchen, cooking facilities) unit, in which case I'd opt for something else nearby.
Overall, 4+ stars