I really wanted to like Ecuador. But for the average cruiser, there's a lot to deal with in order to get here and stay here, and the advantages are really few and far between.
We had a 7 day upwind slog to get here, and we were luckier than most since we actually sailed the whole way having left from Costa Rica. However, that meant that we missed Panama, and we've heard that the cruising in the western islands is among the best in the Pacific, and the provisioning is also excellent.
Once in Ecuador, you are only allowed to stay in the country for 90 days within a 12 month period, and this period of time does not reset should you leave the country. This is often not long enough for boats waiting for March or April to cross the Pacific, hence many people take overland trips into South America or fly home for a period.
The bureaucracy to enter Ecuador is also surprisingly difficult. Regardless of what you may read, you do need an agent in order to arrive, which is an annoyance and somewhat expensive. Upon entry, we had to pay about $35 to the Port Captain, $80 for aduana ($20 to the officials and $60 for a taxi to take our pasports to Manta) and $40 for the pilot. As of March 2010, Puerto Amistad in Bahía de Caráquez is charging a fee to act as an agent - one $50 USD payment when you arrive and another when you leave. Generally these fees are in addition to the ones listed above.
As we discovered when we left, the port captain requires cruisers to go through Puerto Amistad in order to leave, even if you are only moving on to another domestic port. We were able to negotiate with Puerto Amistad to include the port fees (about $18 for us) in with the $50 agency fee, since we did not require immigration or customs and had supplied all our paperwork.
The facilities in Bahía are okay; there is limited provisioning in town, many good restaurants, and easy transportation to Manta where shopping is much better. However, it is a good 45 minutes to Manta by car and much longer by the circuitous bus route.
The mooring fees at Puerto Amistad have also increased substantially over the past two years: as of March 2010 fore-and-aft moorings are $330/month, the dinghy dock fee for anchored boats is $6/day and there is a $1/day fee for unattended anchored boats (this does not cover boat watching services, which are extra). There is now a night security watch in the anchorage, after a string of thefts occurred from anchored boats. However, the high currents in the estuary caused more boats to drag than we have ever seen elsewhere. All were successfully rescued and re-anchored, but some collisions did occur.
All in all, while mainland Ecuador is a beautiful place, we wish we had gone to Panama and traveled to the Galapagos from there instead of coming to Bahía first. Between the high fees, insecure anchorage and difficult bureaucracy, for our money Ecuador is just more trouble than it's worth.