Over a year ago, I booked a pitch session with a highly respected agent at a writer’s conference. My aim was really to see if my then-incomplete YA fantasy was on the right track. I was surprised when she requested the complete manuscript. It took me over 12 months (working around my demanding job, getting a professional manuscript assessment and editing) to send the manuscript. It has been with the agent for about 6 weeks. I know it will take a few months for her to look at it, but do you think she is likely to think I’m unreliable and not worth considering because I took so long? Would it be appropriate to follow up with her after 12 weeks?
I have another question ... As soon as I sent the agent my first YA fantasy manuscript, I started on the sequel. I feel very passionate about the story and the characters and want to continue with them on their journey. Then I wondered if there was any point. If my first manuscript turns out not to be publishable, then the sequel doesn’t have any hope! Maybe I would be better off working on one of my other manuscript ideas? I guess this is a personal choice really, but I would appreciate your advice.
I seriously doubt that an agent will think you're unreliable because you took 12 months to finish your draft - some people take 12 years. What's more likely is that she has put it in the reading pile and will get to it in time. Are you wanting to make contact because you're worried about whether it's arrived or not? If so, I would advise against calling - it is really a super-annoying thing for agents when authors call to see if their submission arrived - but if you really must, sent a simple email (just an enquiry, not an essay) to check. You can presume that your manuscript is not in a priority spot in the queue just because it was requested - only client manuscripts take priority - so it will take a while to be read, but if you haven't already had a letter back saying 'Why are you sending this? Go away!' - because we're quick at sending those letters - you can presume you'll hear in due course.
As to the second question: you can really only write what you want to write - right? You can't force the muse. If it's the sequel that's calling you, then write it - don't worry about whether the first manuscript is published or not. This may not be the right agent or it may not be the right time - and timing is a huge factor in whether books get published - but that doesn't mean you'll never have the right agent or that it will never be the right time.