Should I put two loosely related results into one paper?
Just reading and trying to understand your question made my head spin, most likely due to use of generalization (X, Y, A1, A2), but not only that. Therefore, IMHO, the safest approach to solving this dilemma is to separate results into two papers. The rationale for this approach is the following.


Each paper would have a clear and, thus, easily understandable scope, goals, methodology, results and their interpretation. That would significantly improve readability and overall quality of each paper and chances to form a positive impression.
Since the problems A1 and A2 are "loosely related", shoving them into a single research study simply doesn't make sense from an architectural / logistical / layout perspective. It would be very difficult to present two sub-studies in a synergistic manner ("tell a story", as you put it).
Based on the above-mentioned points, I don't see how combining the studies would make the resulting "study" of higher quality, thus, warranting a publication in a more major conference. Quite the opposite most likely would be true (due to coherence and, thus, readability issues).
Your advisor's recommendation in regard to improving your work is quite strange, to say the least. It is based on the assumption that combining two studies of different scope/topic with weaknesses would make the resulting "study" less weak. If anything, it would make it even weaker, since weakness is one of multitude of characteristics, exhibiting additive properties.