Now that would be fascinating litigation.
But I think it would be incredibly dangerous from a human rights perspective.
First of all, the ECHR can express an opinion that UK legislation isn't compatible with the UK's obligations under the ECHR. It can't actually require the UK to do anything about it. It has soft political power, not hard legal power. Admittedly such an opinion would be persuasive, but ultimately the UK could ignore it and nothing could really be done.
But the reason it would be fascinating is that making any kind of declaration about trans rights (for example, that member countries are required to have a mechanism for people to change their legal gender) requires the ECHR to read between the lines to an incredible extent and find meaning in the treaty that simply wasn't there (because it dates from the 1950s and I think you would be hard pressed to argue that any of the people who drafted it or governments that ratified it believed that humans can change sex).
In my opinion it would be politically unwise for the ECHR to put itself in direct conflict with the UK legal system by taking a position that the UK not respecting its treaty obligations, when there is in fact no obligation in the ECHR to allow people to change their legal sex and never was. Even taking the position that member countries must have a mechanism for allowing people to change their legal sex was a massive, massive overreach.
In my view, if they were to say that it is not enough for the UK to have a mechanism allowing people to change their legal sex, but that someone's legal sex must take priority over their biological sex in all circumstances, no matter how detrimental to other groups (who DO actually have specific protection in the ECHR) would be a bridge too far and could cause the whole edifice to come toppling down. Because as soon as a country like the UK says to the ECHR, "no, fuck off back in your box", other countries might be minded to do the same. And it would certainly make repealing the GRA and its equivalent legislation in other countries much more likely.