I'm not particularly worried for Motorola under Lenovo's ownership. Lenovo has shown itself to be a solid tech company that puts out quality desktops and laptops, and has clearly been interested in improving its mobile footprint throughout the world. Their tablets have been fairly decent so far, with the upcoming Yoga 10 HD+ sounding quite impressive. The company as a whole seems hungry to get more market share, so I think that will translate to strong support for Motorola.
As to your original question, I think the Nexus 5 is a great choice. The battery is average, but it isn't "horrible" as some people are fond of saying. 3-4 hours of screen-on time per charge is to be expected, and with normal moderate use, I get through the day with about 40% of battery to spare. For total battery worriers, just get a wireless charging pad and leave the phone on it whenever you're not using it. The phone itself is superfast and supersmooth, and I would expect typical Nexus support for updates for at least the next 2 years, probably even more.