I'd consider your room/space. If it is a good candidate for beaming (reflected sound) then the Ambeo might be preferable as it would give you nice surround and atmos sound. The Ambeo (with a sub added) arguably has the best overall sound quality of any soundbar - commensurate with its price and physical size.
If your room is not good for beaming then go with the upgraded 3.1 system. FWIW, the HTD Level 3 bookshelf speakers are quite good at their price point. It might take quite a budget jump to get speakers that are noticeably better. Maybe consider just getting the matching HTD Level 3 center speaker and a new receiver, and then add a second sub. That might be the best bang for your buck if your room is on the large size or an open floor plan living room, etc.. (Dual subs isn't necessarily for louder or more bass, but rather for more even distribution of bass sound throughout the room, which typically also increases detail and clarity in the bass range.)
If your room is not good for beaming then go with the upgraded 3.1 system. FWIW, the HTD Level 3 bookshelf speakers are quite good at their price point. It might take quite a budget jump to get speakers that are noticeably better. Maybe consider just getting the matching HTD Level 3 center speaker and a new receiver, and then add a second sub. That might be the best bang for your buck if your room is on the large size or an open floor plan living room, etc.. (Dual subs isn't necessarily for louder or more bass, but rather for more even distribution of bass sound throughout the room, which typically also increases detail and clarity in the bass range.)