Taking stats from the past elections, the most voted party got 39% of the seats with 33% of the votes, and the second party got 34.5% of the seats with 31.7% of the votes. The third and fourth most voted parties got 9.4% and 8.8% of seats with a similar 12.4% and 12.3% of votes. These are all national parties, and it's well known that D'Hondt seat assignment reinforces the most voted parties and punishes everyone else, because the amount of seats in contention on most voting districts is too small. Regional parties have it easier because all their votes are in a small amount of regions, but this doesn't mean they are overrepresented: the percentages of votes and seats match quite well, with some parties being a bit above and others being a bit below. This is because within their regions, these parties are not minorities, so D'Hondt doesn't punish them. The one concession the Spanish system gives to regional parties is a better chance to form their own parliamentary group (important for debate time when discussing laws).

Anyway, I agree that having 50 general election districts (one per province) results in skewed votes. This was done by design as an attempt to have an easier-to-control two party system, and enshrined in the Spanish constitution, so it's not easy to change. It's probably easier to change provinces themselves than the constitution in the current political climate. For instance, merging all provinces in each region together would solve most issues with the voting system, as it would increase the amount of seats in contention.

Regarding the argument about this being a government by a minority of people: the parties that voted for the current government represent roughly 50.5% of the total votes. The current opposition parties represent 45.6% of total votes.