The motivation behind the FTPA was, I think, not unreasonable: with the obvious exception of a Government that is no longer the majority in Parliament, why should it be within the PM's power to set the timing of an election? The present situation where it's become effectively the exact opposite is clearly worse -- it's a nonsense that a minority government serves as the Opposition's pleasure -- but still, I don't think it was an unreasonable problem that FTPA was attempting to address.
Presumably the answer is to beef up the powers of some independent figure whose sole role is to determine, according to some well-defined, objective tests, whether or not a government is functioning effectively; and, if not, to call an election. Historically, that was the role of the Monarch, although I don't think anyone would necessarily be clamouring to beef up their role.
Alternatively, defeats on key votes should be counted as confidence motions of the same status as an explicit confidence motion. Not just (as was the case before) politically equivalent -- a PM who lost a budget vote or a Queen's Speech vote would immediately go to the Queen and seek an election because they'd be seen to have lost a mandate -- but legally equivalent.
That way you could still preserve the idea of taking control over General Elections away from any specific politician, to call or permit on their whim, and give it to the whole House under obvious circumstances. In the present case, for example, it should be clear that Parliament taking control of its own time and out of the hands of government would be grounds for triggering a General Election. Perhaps you could also enforce the rule that a change of PM requires the new government to seek a fresh mandate.