The first observation to make here is there's a difference between a measurable space (that is, a set paired with a $\sigma$-algebra) and a measure space (that is, a measurable space equipped with a measure). I challenge you to find examples where the measure space $(\mathbb{R},\mathscr{B}(\mathbb{R}),\lambda)$ is being studied in a non-trivial manner without implicit reference to $\mathscr{M}(\mathbb{R})$. On the other hand, the measurable space $(\mathbb{R},\mathscr{B}(\mathbb{R}))$ is a natural place to do measure theory.
The issue with $(\mathbb{R},\mathscr{B}(\mathbb{R}),\lambda)$ is it is not a complete measure space. That is, null sets of $\lambda$ need not be measurable. In a sense, once you know what measure you want to put on your measurable space, you should complete it immediately (which you're free to do). Why? Many of the theorems of integration are more naturally stated if you assume completeness, and you're less likely to run into annoying paradoxes. For example, if you give me a set $B \in \mathscr{M}(\mathbb{R}) \setminus \mathscr{B}(\mathbb{R})$, then $\chi_{B}$ is Lebesgue but not Borel measurable. Nonetheless, I can find a sequence $(\varphi_{n})_{n \in \mathbb{N}}$ of smooth functions such that $\varphi_{n}(x) \to \chi_{B}(x)$ for almost every $x \in \mathbb{R}$.
The way I think of this is, once you have a measure in mind, you should complete the space. I haven't come across a counter-example to this rule of thumb yet.
While I don't think $(\mathbb{R},\mathscr{B}(\mathbb{R}),\lambda)$ is a very interesting measure space, $(\mathbb{R},\mathscr{B}(\mathbb{R}))$ is an important measurable space. This is easiest to see in the context of probability.
Suppose we have a probability space $(\Omega,\mathcal{F},\mathbb{P})$ and we're interested in a function $X : \Omega \to \mathbb{R}$, as one often is. Probably we're not interested in knowing $X$ pointwise, that is, in understanding the function $\omega \mapsto X(\omega)$, since somewhat implicit in the set-up of a probability space is we don't know which outcomes $\omega$ in $\Omega$ we're dealing with. The set-up of measure-theoretic probability is instead that we would like to know $\mathbb{P}\{X \in A\}$ for a rich enough collection of subsets $A$ of $\mathbb{R}$. This is only well-defined if the events $\{X \in A\}$ are in $\mathcal{F}$ to begin with. In other words, we need to understand a little bit about the push forward $\sigma$-algebra $\mathcal{F}_{X} = \{A \subseteq \mathbb{R} \, \mid \, X^{-1}(A) \in \mathcal{F}\}$.
What sets should $\mathcal{F}_{X}$ contain in general? This is up to how you want to define probability theory. The standard set-up is $X$ is a random variable if the push forward $\sigma$-algebra contains $\mathscr{B}(\mathbb{R})$. Why? Well, one way to think about random variables it to ask that, at the very least, we should be able to compute $\mathbb{P}\{X \leq c\}$ for arbitrary real numbers $c$. More rigorously, we should demand that $\{X \leq c\} \in \mathcal{F}$ (or $(-\infty,c] \in \mathcal{F}_{X}$) independently of the choice of $c$.
However, the collection $\{(\infty,c] \, \mid \, c \in \mathbb{R}\}$ generates $\mathscr{B}(\mathbb{R})$ so if the $\mathcal{F}_{X} \supseteq \{(-\infty,c] \, \mid \, c \in \mathbb{R}\}$, then it contains $\mathscr{B}(\mathbb{R})$. In fact, the following result holds:
The following are equivalent:
1) $\mathscr{B}(\mathbb{R})\subseteq \mathcal{F}_{X}$
2) $\forall c \in \mathbb{R} \quad \{X \leq c\} \in \mathcal{F}$
3) $\forall c \in \mathbb{R} \quad \{X < c\} \in \mathcal{F}$
4) $\forall c \in \mathbb{R} \quad \{X \geq c\} \in \mathcal{F}$
5) $\forall c \in \mathbb{R} \quad \{X > c\} \in \mathcal{F}$
6) If $U \subseteq \mathbb{R}$ is open, then $\{X \in U\} \in \mathcal{F}$
7) If $C \subseteq \mathbb{R}$ is closed, then $\{X \in C\} \in \mathcal{F}$
The point is if you want to be able to ask questions about random variables involving the topology (or ordering) of $\mathbb{R}$, then you need the random variable to be measurable from $(\Omega,\mathcal{F},\mathbb{P})$ into $(\mathbb{R},\mathscr{B}(\mathbb{R}))$ at a minimum. This is why the modern theory of probability defines (real-valued) random variables in terms of $(\mathbb{R},\mathscr{B}(\mathbb{R}))$.