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What tools should I choose for a given task

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I have extensive experience in software development in general, now I want to try simple game development, I know what result I want, but not sure what tools and what development flow should I choose and I don't want to invent a wheel.
More details on what I want:
Programming language: Java;
I would prefer 2D, but 3D is also ok.
I want to create game with really simple graphics, and good physics support. What is in this sample (graphics and physics) is sufficient: http://www.jbox2d.org/demos/washingmachine.html
BUT, I want to use animations of characters (ragdolls in this case) which could be affected by physics, or interchanged between physics generated animations (pendulum, friction, bouncing and so on) and predefined animations (character walking, waving, sitting, running, climbing stairs).
Problem is I could not find any software that would help to create those animations (I mean sprites is not a solution - I need to have skeleton!)!
And I really do not want to CODE those animations by providing coordinates of joints
and moving them in time, especially because I'm thinking about A LOT of animations! They should be created with some GUI tool :)
The best I can think of is creating object animations in some 3D software, then somehow mapping 3d objects to character skeleton definition, loading animations in game and then interchangeably applying predefined animations or physics engine generated animations.
I would limit character movements in 3D world to constant Z-axis for 2D-like game look&feel.
Since all the work (graphics, animations and programming) will be done by me, I'm seeking for a simplest and least overall work requiring solution.
Any suggestions for tools or tips on technique, game engines? :)

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You can create mesh, skeleton and animate in most of 3D modelling software, from free like Blender, through shareware like Milkshape3D, to professional software like 3DS Max or Maya.

Then for skeletal animations you need to choose some format that supports skeletal animated mesh, like MD5, MD3, Collada, and much much more other formats.

Most engines have their exporters to these formats and knows how to use them - e.g. if you take ID Tech 5 - you'll also get MD5 exporter and the engine will know how to use and load MD5Mesh and MD5Anim files.
Or you can write your own skeletal animation stuff (or even skeletal animation library) - it isn't that hard (math behind it and implementation) and there are lots of sources on it afaic :)

Here on this site are some MD5 tutorials and MD5 format description http://tfc.duke.free.fr/coding/md5-specs-en.html

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