We have to point out some simple remark of capital importance. First of all, the lagrangian is not defined as $L = T - V$. This turns out to be true only on a riemannian manifold; the fact this is almost always true in classical mechanics is an "accident" due to the postulates of classical (non relativistic) mechanics. For the most precise definition of the lagrangian, see my answer to this question.
Here we are interested to the fact the lagrangian is by definition the function that satisfies the Euler-Lagrange equations along the curves of motions and so reproduce the equations of motion.
In fact, if you follow, for example, Landau's treatment (see References), you can see how the form of lagrangian is established from a physical point of view. Assume the action principle and denote with $S$ the action for our system and with $q$ the set of generalized coordinates we are using. Then the lagrangian is, by definition, the function such that the integral
$$S = \int_{t_0}^{t_1} L( \dot q, q, t ) \mbox{d}t$$
get an extremal value along the trajectories of the motion. By varying $S$, we find Euler-Langrange equations and the fact that $L$ is defined up to a total derivative with respect to time of an arbitrary differentiable function of time and coordinates, $f(q,t)$. Why is $L$ a function of $\dot q, q$ and $t$ but not, for example, of $\ddot q$? Because newtonian mechanics postulates state that the state of a system is completely determined by the knowledge of all positions and velocities of its constituents at a given instant. Now we would establish the functional form of $L$. In order to do this, we consider the galilean postulate of relativity. We can rephrase it in a more suitable form for our goals:
Postulate(Galilean relativity) There exists a class of frame of reference respect to which the space is homogeneus and isotropic. In those frames, equations of motion retain the same form.
Consider a free-moving particle in an inertial frame of reference. Let's indicate with $\mathbf{r}$ its position and with $\mathbf{v}$ its velocity in such a frame. Since there are no preferred points in the space (nor in time: time flows in the same manner for all observers - i.e. in all frames - in newtonian mechanics), $L$ can't depend on $\mathbf{r}$ or $t$. So it is a function of $\mathbf{v}$ only. Moreover, in virtues of absence of preferred directions, it depends only on $v^2$. Hence $L = L(v^2)$. It follows that
$$ \frac{\partial L}{\partial{\mathbf{r}}} = 0 \implies \frac{\mbox{d}}{\mbox{d}t} \frac{\partial L}{\partial{\mathbf v}} = 0$$.
This implies that $\mathbf{v} = \mbox{constant}$ also. From here we obtain Galilei's transformations. Take two inertial frames of reference, $K$ and $K'$, moving one respect to other with a small velocity $\mathbf{a}$. In $K'$ lagrangian is $L'(v'^2)$, while in $K$ is $L(v^2)$. Since the form of equation of motion must be the same,
$$L'(v'^2) = L(v^2) = L(v^2 + 2\mathbf{a \cdot v} + a^2)$$
Expanding the last member in series of powers of $\mathbf{a}$ and retaining only the first order term, we get
$$L'(v'^2) = L(v^2) + \frac{\partial L}{\partial{v^2}} 2 \mathbf{a \cdot v}.$$
The last term in RHS is a total derivative with respect to time. From the above remark, this means that $\frac{\partial L}{\partial{v^2}}$ can't depend on $v^2$ and hence
$$L = a v^2.$$
We reproduce known equation of motion for a free moving particle if we set $a=m/2$.
Now, if we take a compound system and we separate its constituents in such a way that interactions turn out to be negligible, then for each constituent we can write a free-body lagrangian and the lagrangian for the whole system will the sum of all of them. This means that the free-body lagrangian (in an inertial frame of reference) enjoys the expected characteristics for a kinetic energy.
Finally, consider a system in which interactions between particles are not negligible. We make the following ansatz:
$$L = \sum_\alpha \frac{m_\alpha v_\alpha^2}{2} - V( \mathbf{r_1,r_2 \dots} ).$$
($V$ is a differentiable function of coordinate.)
Using Euler-Langrange equations, we get
$$m_\alpha \frac{\mbox{d}\mathbf{v}_\alpha}{\mbox{d}t} = -\frac{\partial V}{\partial \mathbf{r_\alpha}},$$
that is Newton's Second Law. (at least when masses are fixed.) So our ansatz works.
We have to note that in order to derive the form of $L$, we have used the postulates of newtonian mechanics. So our result is no longer valid when those do not apply. In particular, $L = T - V$ is only a particular case and is not a good definition for $L$.
A side question is: does $L$ have a physical significance? No. We measure
the equations of motion, not the lagrangian! So the form of $L$ is not important, provided that it reproduces the equations of motion.
Now, the energy. I think you would mean that the hamiltonian, often written as $H = T + V$, makes more sense. In effect, energy is measured quantity, but the hamiltonian is not defined as $H = T + V$. It is, by definition, the Legendre transform of $L$ with respect to $\mathbf{v}$ ($\dot q$ in general). It turns out to be the energy only in the case $L = T - V$ and, in addition, $T$ takes the form $T = \sum_{i,j} a_{ij}(q, t) \dot q_i \dot q_j$, i.e. is a symmetric quadratic form in $\dot q$ whose coefficients are function of $q$ and $t$ only and are symmetric in $i,j$.
References
L. Landau, E. Lifshitz, Mechanics
V. Arnold, Mathematical methods of classical mechanics