The A2000 is sturdier and better built over all. The chips and other electronic components are either socketed or soldered in plate through holes which are a lot easier to desolder and replace than surface mounted chips.
The battery in the A4000 is right near the simm sockets, buster and other sensitive areas. I got mine out before it did much damage but I did have to clean up a bit to get it to recognize all the memory simms. The A4000's A3640 CPU card has 5 surface mounted electrolytic capacitiors and 3 are usually mounted with the polarity reversed which makes them tend to leak and cause damage. It was one of the ones with correct polarity next to the 68040 that leaked and killed my first A3640, ironically.
Of all the big box Amigas, the A4000 is the most ergonomic and space effecient. The internal 5.2" drive bay helps a lot compared to the A3000. It still takes up a lot of room but a lot less than an A2000. But, hey, the Amiga came out long before the era of laptops and way before the era of smart phones and, if you want one, you are going to have to set aside some space for it.