There will always be solutions that can't be analytical. For example, any model of more than two bodies without any special constraints, cannot be solved analytically. From the gravitational interactions between three planets to three particles interacting (electromagnetically or otherwise) in quantum theory. To have mathematically analytical solutions, certain simple constraints need to be applied, regardless of the system you are modeling. This is why physical theories or analysis (calculus) in general are taught using simple models. Spherical, cubic, or cylindrical models, generally with two bodies, or otherwise special coordinate constraints are placed on larger numbers of bodies.
Some problems, whether higher degree polynominals, certain integrals, or many differential equations simply lack a closed mathematical expression to solve them. This is when numerics steps in (pun intended). Numerics is a huge branch of mathematics that finds solutions to problems through approximating them. How exact you want to approximate it is up to you (check out the Newtonian approximation to solve x-intercepts as an example). You can run your algorithm as long as you like, and you can also calculate your error and even prove that it converges to zero. If anything, this is more like the real world. If you repeat an experiment over and over, even trying to repeat it exactly, you will usually get slightly different values. You need to calculate your errors and see if these measurements fall within your values given by your theoretical model.
Now interestingly enough there exists a hybrid of the two systems. Finding an approximation of a problem that is an analytical function. This covers perturbation theory. One good example of this is the nuclear shell model. To reproduce the "magic numbers" a couple of analytical functions were combined that gave good results. Take a look at the deformed harmonic oscillator model (Woods-Saxon is interesting also).
Are these models flawed or wrong because they are approximated? No, they give the results needed for calculations, within a tolerance that can be calculated. They are no more wrong than Newtonian mechanics is for a slow body moving in a flat space-time.
To conclude, there will always be problems that cannot be solved analytically, a proof can even be offered to argue that for many of them, and there will be some surprises occasionally (a new analytical solution to a given problem when only some very special constraints are applied), but in the end we have to accept that the universe isn't a perfect sphere, in a vacuum, with only two bodies in it to calculate, and that a constraint free many-body problem will always have to be solved numerically.