1: Is this a "surprised" skill check? Does the cleric know that she's going to have to do a skill check in advance?
2: Closely related to #1, is there a lack of time to cast the spell? You may know it's coming but simply not have the time
3: Would it be socially awkward? It's not nice to try to convince someone to do something (diplomacy check) or try to see if they are lying (insight check) and start spell-casting in the middle of a conversation.
These are definitely reasonable limitations. Neither our Cleric nor our Druid have this cantrip, so it's a non-issue for us, but in the past I have usually thought that the main limitation of Guidance is with
reactive checks and with
group checks.
Group checks are the unavoidable limitation. If you have
one person who knows the spell, you have
one person at a time who can benefit from it. Sure in some cases everyone can queue, for example if they all need to jump a chasm they can of course cast+jump+cast+jump+cast+jump... one character at a time. But when the whole group is moving silently in the dungeon (stealth), or they all navigate the wilderness (survival), or they all climb a mountain (athletics), how exactly can you tell
when each one is making the check?
However, even reactive checks can benefit from
Guidance if the spell is cast beforehand. It only lasts one minute, so if a player really wants to exploit the RAW of this cantrip, she could
repeatedly cast this cantrip once per minute, dawn to dusk, and it would really cover every possible check, except those during combat rounds. Narratively speaking, this is a truly dorky situation, and I believe that the vast majority of players simply refuse to accept this to become their normal course of action, simply because it narratively sucks. And that's why apparently Guidance isn't much of a problem after all, because the players chose not to exploit it,
not because it's good design.