There are several antecedents you may want to take in consideration to approach an aswer for this question here:
- Queretero as such was re-founded on 1537 by the local Otomi leader "Conin" who was baptised by the spanish church and named afterwards "Fernando de Tapia". Using his friendship with the spanish caciques, he managed to secure the location for the locals and at that time, Queretaro was known to be a "city for the indians".
- Around 1550, it was probably the most transited city, it was called the gateway of the Bajio and was a forced stop for convoys coming and going from Zacatecas (lots of silver and copper mines), to México City, Puebla and Veracruz.
- Around 1680 it became the third most economically important city in "Nueva España" right behind Puebla and México city thanks to the dedication of the temple of the consacration presided by Carlos de Sigüenza y Góngora. Seen from the cultural point of view Queretaro was for a long time aknowledged as the cradle of novo-hispanic culture.
- By the 18th century, the city became more relevant industry-wise, during this time, the city was transformed by the large quantities of infrastructure works that took place such as the infamous aqueduct that was built around 1730.
Then, by the 1800's we had a well-developed city with proper infrastructure, very close to the capital, in an strategic location and with the cultural personality and history to house some of the greatest social movements in the history of the country (you know, like the independence and the sort). All resulting in a very appealing stage for an alternate capital.
Also important but probabaly not very relevant at the time of the capital-relocation decision, is the fact that Queretaro is located in a geostable region, a feat that some strategic industries (such as datacenters) value a lot these days, as a matter of fact Queretaro is today one of the largest industrial centers in the country.
So because of all this, in my opinion (as a mexican and as a fan of history) Queretaro was and still would be one of the first choices for an alternate mexican capital.