It's difficult to say without any idea of budget preferences, etc. to make any recommendations.
But your options to Mérida are many, now that Mexico has LLCs (and MX is down), and for a longer trip there is even the deluxe bus service (e.g. ADO Platino
or ADO GL
- Gran Lujo with onboard IFE and Wireless, etc.) (It's a nineteen hour slog, so air is definitely more practical.)